rs1906252

Variant names:

• chr6-98102413-C-A
• rs1906252
• ENST00000606913.5:n.240+3143C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-98102413-C-A
• chr6-98102413-C-G
• chr6-98102413-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000606913.5(ENSG00000271860):​n.240+3143C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 151,410 control chromosomes in the GnomAD database, including 12,671 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.39 (12671 hom., cov: 30)
• Consequence: ENSG00000271860 ENST00000606913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.292
• Publications: 21 publications found

Genes affected

ENSG00000271860 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000606913.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000271860	ENST00000606913.5	TSL:5	n.240+3143C>A		intron	N/A
	ENSG00000271860	ENST00000607032.1	TSL:3	n.410+3143C>A		intron	N/A
	ENSG00000271860	ENST00000607823.5	TSL:5	n.352+3143C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59519 AN: 151296 Hom.: 12676 Cov.: 30

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.393 AC: 59507 AN: 151410 Hom.: 12671 Cov.: 30 AF XY: 0.391 AC XY: 28884 AN XY: 73962

African (AFR) AF: 0.231 AC: 9530 AN: 41278

American (AMR) AF: 0.351 AC: 5343 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.538 AC: 1866 AN: 3468

East Asian (EAS) AF: 0.408 AC: 2095 AN: 5132

South Asian (SAS) AF: 0.272 AC: 1306 AN: 4808

European-Finnish (FIN) AF: 0.488 AC: 5069 AN: 10378

Middle Eastern (MID) AF: 0.524 AC: 153 AN: 292

European-Non Finnish (NFE) AF: 0.485 AC: 32911 AN: 67828

Other (OTH) AF: 0.396 AC: 830 AN: 2096

Alfa AF: 0.453 Hom.: 8315

Bravo AF: 0.379

Asia WGS AF: 0.271 AC: 945 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.17
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs1906252; hg19: chr6-98550289;