chr11-59456671-T-G

Variant names:

• chr11-59456671-T-G
• rs7943953

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 0.609 in 152,066 control chromosomes in the GnomAD database, including 29,045 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 0.61 (29045 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.725 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: 0.609 AC: 92559 AN: 151948 Hom.: 29058 Cov.: 32

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.609 AC: 92567 AN: 152066 Hom.: 29045 Cov.: 32 AF XY: 0.612 AC XY: 45514 AN XY: 74322

African (AFR) AF: 0.450 AC: 18668 AN: 41466

American (AMR) AF: 0.593 AC: 9063 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.708 AC: 2456 AN: 3470

East Asian (EAS) AF: 0.738 AC: 3810 AN: 5162

South Asian (SAS) AF: 0.745 AC: 3588 AN: 4814

European-Finnish (FIN) AF: 0.664 AC: 7028 AN: 10582

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.673 AC: 45737 AN: 67970

Other (OTH) AF: 0.621 AC: 1313 AN: 2116

Alfa AF: 0.636 Hom.: 50598

Bravo AF: 0.596

Asia WGS AF: 0.670 AC: 2332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.21
DANN	Benign	0.81
PhyloP100		-2.1
PromoterAI		0.010	Neutral

Splicing

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

Other links and lift over

dbSNP: rs7943953; hg19: chr11-59224144;