11-73973170-A-G

Variant names:

• chr11-73973170-A-G
• rs655717

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 0.56 in 152,044 control chromosomes in the GnomAD database, including 25,752 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 0.56 (25752 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.806 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: 0.560 AC: 85142 AN: 151926 Hom.: 25731 Cov.: 32

Gnomad AFR AF: 0.814

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.560 AC: 85207 AN: 152044 Hom.: 25752 Cov.: 32 AF XY: 0.557 AC XY: 41396 AN XY: 74312

African (AFR) AF: 0.813 AC: 33750 AN: 41496

American (AMR) AF: 0.526 AC: 8038 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.446 AC: 1550 AN: 3472

East Asian (EAS) AF: 0.433 AC: 2240 AN: 5170

South Asian (SAS) AF: 0.402 AC: 1933 AN: 4814

European-Finnish (FIN) AF: 0.497 AC: 5250 AN: 10556

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.454 AC: 30826 AN: 67948

Other (OTH) AF: 0.534 AC: 1124 AN: 2106

Alfa AF: 0.478 Hom.: 78965

Bravo AF: 0.575

Asia WGS AF: 0.438 AC: 1522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.67
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs655717; hg19: chr11-73684215;