11-643683-T-C

Variant names:

• chr11-643683-T-C
• rs4331145

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 0.509 in 152,106 control chromosomes in the GnomAD database, including 20,003 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 0.51 (20003 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.735 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: 0.509 AC: 77396 AN: 151988 Hom.: 19980 Cov.: 34

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.509 AC: 77469 AN: 152106 Hom.: 20003 Cov.: 34 AF XY: 0.512 AC XY: 38099 AN XY: 74366

African (AFR) AF: 0.448 AC: 18585 AN: 41472

American (AMR) AF: 0.544 AC: 8330 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1731 AN: 3464

East Asian (EAS) AF: 0.755 AC: 3892 AN: 5158

South Asian (SAS) AF: 0.590 AC: 2848 AN: 4826

European-Finnish (FIN) AF: 0.482 AC: 5113 AN: 10598

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.518 AC: 35220 AN: 67968

Other (OTH) AF: 0.509 AC: 1076 AN: 2116

Alfa AF: 0.503 Hom.: 3824

Bravo AF: 0.511

Asia WGS AF: 0.627 AC: 2181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.36
DANN	Benign	0.21
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4331145; hg19: chr11-643683;