chr11-63971170-T-G

Variant names:

• chr11-63971170-T-G
• rs11231662

Variant summary

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

The variant allele was found at a frequency of 0.28 in 152,060 control chromosomes in the GnomAD database, including 7,604 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 0.28 (7604 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.135
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42622 AN: 151942 Hom.: 7597 Cov.: 32

Gnomad AFR AF: 0.0825

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.0477

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.280 AC: 42632 AN: 152060 Hom.: 7604 Cov.: 32 AF XY: 0.279 AC XY: 20739 AN XY: 74322

African (AFR) AF: 0.0823 AC: 3417 AN: 41518

American (AMR) AF: 0.224 AC: 3419 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1629 AN: 3468

East Asian (EAS) AF: 0.0478 AC: 248 AN: 5186

South Asian (SAS) AF: 0.314 AC: 1514 AN: 4818

European-Finnish (FIN) AF: 0.413 AC: 4355 AN: 10556

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.398 AC: 27004 AN: 67930

Other (OTH) AF: 0.282 AC: 594 AN: 2108

Alfa AF: 0.330 Hom.: 3990

Bravo AF: 0.255

Asia WGS AF: 0.147 AC: 515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.5
DANN	Benign	0.61
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs11231662; hg19: chr11-63738642;