rs61199332

Variant names:

• chr8-11573132-C-T
• rs61199332

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.0602 in 152,304 control chromosomes in the GnomAD database, including 563 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.060 (563 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter P:1 B:3
• Conservation: PhyloP100: -0.0330
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 8-11573132-C-T is Benign according to our data. Variant chr8-11573132-C-T is described in ClinVar as Benign. ClinVar VariationId is 12321.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0600 AC: 9134 AN: 152186 Hom.: 555 Cov.: 33

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0306

Gnomad ASJ AF: 0.0374

Gnomad EAS AF: 0.00711

Gnomad SAS AF: 0.0402

Gnomad FIN AF: 0.00847

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0224

Gnomad OTH AF: 0.0550

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

GnomAD4 genome AF: 0.0602 AC: 9168 AN: 152304 Hom.: 563 Cov.: 33 AF XY: 0.0591 AC XY: 4402 AN XY: 74478

African (AFR) AF: 0.159 AC: 6589 AN: 41534

American (AMR) AF: 0.0304 AC: 466 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0374 AC: 130 AN: 3472

East Asian (EAS) AF: 0.00713 AC: 37 AN: 5192

South Asian (SAS) AF: 0.0396 AC: 191 AN: 4820

European-Finnish (FIN) AF: 0.00847 AC: 90 AN: 10628

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0224 AC: 1527 AN: 68034

Other (OTH) AF: 0.0545 AC: 115 AN: 2112

Alfa AF: 0.0433 Hom.: 133

Bravo AF: 0.0662

Asia WGS AF: 0.0390 AC: 134 AN: 3478

ClinVar

ClinVar submissions as Germline

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
1	-	1	Maturity-onset diabetes of the young type 11 (2)
-	-	1	BLK-related disorder (1)
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.4
DANN	Benign	0.76
PhyloP100		-0.033

Splicing

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

Other links and lift over

dbSNP: rs61199332; hg19: chr8-11430641;