rs149157547

Variant names:

• chr10-96192322-CTACT-C
• rs149157547
• NM_013314.4:c.1252-234_1252-231delAGTA

Your query was ambiguous. Multiple possible variants found:

• chr10-96192322-CTACT-C
• chr10-96192322-CTACT-CTACTTACT

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_013314.4(BLNK):​c.1252-234_1252-231delAGTA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0702 in 152,152 control chromosomes in the GnomAD database, including 720 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.070 (720 hom., cov: 31)
• Consequence: BLNK NM_013314.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.663
• Publications: 0 publications found

Genes affected

BLNK (HGNC:14211): (B cell linker) This gene encodes a cytoplasmic linker or adaptor protein that plays a critical role in B cell development. This protein bridges B cell receptor-associated kinase activation with downstream signaling pathways, thereby affecting various biological functions. The phosphorylation of five tyrosine residues is necessary for this protein to nucleate distinct signaling effectors following B cell receptor activation. Mutations in this gene cause hypoglobulinemia and absent B cells, a disease in which the pro- to pre-B-cell transition is developmentally blocked. Deficiency in this protein has also been shown in some cases of pre-B acute lymphoblastic leukemia. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, May 2012]

ZNF518A (HGNC:29009): (zinc finger protein 518A) The protein encoded by this gene is a member of the krueppel C2H2-type zinc finger protein family. The encoded protein contains five zinc fingers and is likely a nuclear transcriptional regulator. Numerous transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Aug 2016]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP6: Variant 10-96192322-CTACT-C is Benign according to our data. Variant chr10-96192322-CTACT-C is described in ClinVar as Benign. ClinVar VariationId is 1224035.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013314.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BLNK	NM_013314.4	MANE Select	c.1252-234_1252-231delAGTA		intron	N/A	NP_037446.1	Q8WV28-1
	BLNK	NM_001114094.2		c.1183-234_1183-231delAGTA		intron	N/A	NP_001107566.1	Q8WV28-2
	BLNK	NM_001258440.2		c.1096-234_1096-231delAGTA		intron	N/A	NP_001245369.1	Q8WV28-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BLNK	ENST00000224337.10	TSL:1 MANE Select	c.1252-234_1252-231delAGTA		intron	N/A	ENSP00000224337.6	Q8WV28-1
	BLNK	ENST00000371176.7	TSL:1	c.1183-234_1183-231delAGTA		intron	N/A	ENSP00000360218.2	Q8WV28-2
	BLNK	ENST00000413476.6	TSL:1	c.1096-234_1096-231delAGTA		intron	N/A	ENSP00000397487.2	Q8WV28-3

Frequencies

GnomAD3 genomes AF: 0.0703 AC: 10686 AN: 152034 Hom.: 722 Cov.: 31

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0452

Gnomad ASJ AF: 0.0395

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0320

Gnomad FIN AF: 0.0171

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0292

Gnomad OTH AF: 0.0762

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0702 AC: 10688 AN: 152152 Hom.: 720 Cov.: 31 AF XY: 0.0692 AC XY: 5149 AN XY: 74408

African (AFR) AF: 0.178 AC: 7365 AN: 41486

American (AMR) AF: 0.0450 AC: 689 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0395 AC: 137 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5184

South Asian (SAS) AF: 0.0312 AC: 150 AN: 4810

European-Finnish (FIN) AF: 0.0171 AC: 182 AN: 10614

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0291 AC: 1981 AN: 67980

Other (OTH) AF: 0.0754 AC: 159 AN: 2108

Alfa AF: 0.0560 Hom.: 59

Bravo AF: 0.0772

Asia WGS AF: 0.0220 AC: 78 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.66
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs149157547; hg19: chr10-97952078;