chr7-1173491-A-G

Variant names:

• chr7-1173491-A-G
• rs1543985

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 0.696 in 152,166 control chromosomes in the GnomAD database, including 38,039 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 0.70 (38039 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.501
• Publications: 15 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 = 0.867 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.696 AC: 105806 AN: 152048 Hom.: 37988 Cov.: 33

Gnomad AFR AF: 0.875

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.650

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.696 AC: 105908 AN: 152166 Hom.: 38039 Cov.: 33 AF XY: 0.692 AC XY: 51476 AN XY: 74386

African (AFR) AF: 0.875 AC: 36329 AN: 41534

American (AMR) AF: 0.626 AC: 9577 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2226 AN: 3470

East Asian (EAS) AF: 0.456 AC: 2354 AN: 5158

South Asian (SAS) AF: 0.610 AC: 2946 AN: 4828

European-Finnish (FIN) AF: 0.650 AC: 6871 AN: 10572

Middle Eastern (MID) AF: 0.627 AC: 183 AN: 292

European-Non Finnish (NFE) AF: 0.639 AC: 43430 AN: 68000

Other (OTH) AF: 0.657 AC: 1389 AN: 2114

Alfa AF: 0.652 Hom.: 37946

Bravo AF: 0.700

Asia WGS AF: 0.560 AC: 1947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.11
DANN	Benign	0.35
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs1543985; hg19: chr7-1213127;