rs676653

Variant names:

• chr11-67572065-T-A
• rs676653

Your query was ambiguous. Multiple possible variants found:

• chr11-67572065-T-A
• chr11-67572065-T-C
• chr11-67572065-T-G

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 0.895 in 152,184 control chromosomes in the GnomAD database, including 61,028 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 0.90 (61028 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.911 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: 0.895 AC: 136160 AN: 152066 Hom.: 61008 Cov.: 32

Gnomad AFR AF: 0.871

Gnomad AMI AF: 0.940

Gnomad AMR AF: 0.894

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.922

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.917

Gnomad OTH AF: 0.903

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

GnomAD4 genome AF: 0.895 AC: 136235 AN: 152184 Hom.: 61028 Cov.: 32 AF XY: 0.893 AC XY: 66465 AN XY: 74392

African (AFR) AF: 0.871 AC: 36154 AN: 41508

American (AMR) AF: 0.894 AC: 13661 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.910 AC: 3158 AN: 3472

East Asian (EAS) AF: 0.871 AC: 4501 AN: 5168

South Asian (SAS) AF: 0.921 AC: 4439 AN: 4820

European-Finnish (FIN) AF: 0.839 AC: 8879 AN: 10582

Middle Eastern (MID) AF: 0.888 AC: 261 AN: 294

European-Non Finnish (NFE) AF: 0.917 AC: 62417 AN: 68032

Other (OTH) AF: 0.902 AC: 1908 AN: 2116

Alfa AF: 0.904 Hom.: 7726

Bravo AF: 0.898

Asia WGS AF: 0.900 AC: 3133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.19
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs676653; hg19: chr11-67339536;