rs6589964

Variant names:

• chr11-122999975-A-C
• rs6589964

Your query was ambiguous. Multiple possible variants found:

• chr11-122999975-A-C
• chr11-122999975-A-T

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 0.538 in 152,082 control chromosomes in the GnomAD database, including 22,631 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 0.54 (22631 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.771
• Publications: 37 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.624 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: 0.538 AC: 81803 AN: 151962 Hom.: 22601 Cov.: 32

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.515

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

GnomAD4 genome AF: 0.538 AC: 81874 AN: 152082 Hom.: 22631 Cov.: 32 AF XY: 0.532 AC XY: 39548 AN XY: 74346

African (AFR) AF: 0.630 AC: 26130 AN: 41464

American (AMR) AF: 0.376 AC: 5738 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.582 AC: 2017 AN: 3468

East Asian (EAS) AF: 0.538 AC: 2783 AN: 5176

South Asian (SAS) AF: 0.487 AC: 2350 AN: 4824

European-Finnish (FIN) AF: 0.489 AC: 5168 AN: 10564

Middle Eastern (MID) AF: 0.541 AC: 158 AN: 292

European-Non Finnish (NFE) AF: 0.527 AC: 35827 AN: 68000

Other (OTH) AF: 0.519 AC: 1094 AN: 2106

Alfa AF: 0.533 Hom.: 88271

Bravo AF: 0.538

Asia WGS AF: 0.489 AC: 1700 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.55
DANN	Benign	0.27
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs6589964; hg19: chr11-122870683;