rs1675090

Variant names:

• chr11-62172634-G-A
• rs1675090

Your query was ambiguous. Multiple possible variants found:

• chr11-62172634-G-A
• chr11-62172634-G-C

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 0.543 in 151,304 control chromosomes in the GnomAD database, including 22,755 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 (22755 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.270
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82119 AN: 151198 Hom.: 22738 Cov.: 30

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.543 AC: 82182 AN: 151304 Hom.: 22755 Cov.: 30 AF XY: 0.538 AC XY: 39746 AN XY: 73860

African (AFR) AF: 0.638 AC: 26340 AN: 41264

American (AMR) AF: 0.549 AC: 8353 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1441 AN: 3466

East Asian (EAS) AF: 0.416 AC: 2135 AN: 5134

South Asian (SAS) AF: 0.566 AC: 2722 AN: 4806

European-Finnish (FIN) AF: 0.370 AC: 3805 AN: 10270

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.526 AC: 35701 AN: 67842

Other (OTH) AF: 0.538 AC: 1130 AN: 2102

Alfa AF: 0.532 Hom.: 68341

Bravo AF: 0.554

Asia WGS AF: 0.525 AC: 1829 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	15
DANN	Benign	0.89
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs1675090; hg19: chr11-61940106;