rs1174943

Variant names:

• chr7-21967500-G-A
• rs1174943

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 0.873 in 152,084 control chromosomes in the GnomAD database, including 58,120 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 0.87 (58120 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0690
• Publications: 1 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 = 0.936 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: 0.873 AC: 132619 AN: 151966 Hom.: 58068 Cov.: 30

Gnomad AFR AF: 0.944

Gnomad AMI AF: 0.750

Gnomad AMR AF: 0.885

Gnomad ASJ AF: 0.806

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.784

Gnomad FIN AF: 0.888

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.850

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

GnomAD4 genome AF: 0.873 AC: 132729 AN: 152084 Hom.: 58120 Cov.: 30 AF XY: 0.874 AC XY: 64998 AN XY: 74334

African (AFR) AF: 0.944 AC: 39162 AN: 41502

American (AMR) AF: 0.885 AC: 13520 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.806 AC: 2796 AN: 3468

East Asian (EAS) AF: 0.879 AC: 4541 AN: 5164

South Asian (SAS) AF: 0.783 AC: 3772 AN: 4818

European-Finnish (FIN) AF: 0.888 AC: 9383 AN: 10572

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.836 AC: 56822 AN: 67972

Other (OTH) AF: 0.852 AC: 1798 AN: 2110

Alfa AF: 0.846 Hom.: 164306

Bravo AF: 0.877

Asia WGS AF: 0.825 AC: 2871 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	1.6
DANN	Benign	0.74
PhyloP100		-0.069

Splicing

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

Other links and lift over

dbSNP: rs1174943; hg19: chr7-22007118;