11-62907131-C-G

Variant names:

• chr11-62907131-C-G
• rs4963323

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 0.132 in 152,150 control chromosomes in the GnomAD database, including 1,601 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 0.13 (1601 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.23 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: 0.132 AC: 20008 AN: 152032 Hom.: 1599 Cov.: 32

Gnomad AFR AF: 0.0361

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.132 AC: 20017 AN: 152150 Hom.: 1601 Cov.: 32 AF XY: 0.134 AC XY: 9959 AN XY: 74396

African (AFR) AF: 0.0359 AC: 1492 AN: 41530

American (AMR) AF: 0.149 AC: 2280 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 709 AN: 3468

East Asian (EAS) AF: 0.242 AC: 1251 AN: 5178

South Asian (SAS) AF: 0.172 AC: 831 AN: 4818

European-Finnish (FIN) AF: 0.175 AC: 1850 AN: 10578

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11170 AN: 67986

Other (OTH) AF: 0.140 AC: 296 AN: 2110

Alfa AF: 0.0817 Hom.: 120

Bravo AF: 0.127

Asia WGS AF: 0.176 AC: 612 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.27
DANN	Benign	0.55
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs4963323; hg19: chr11-62674603;