rs1174943

Positions:

• chr7-21967500-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.944

Gnomad4 AMR AF: 0.885

Gnomad4 ASJ AF: 0.806

Gnomad4 EAS AF: 0.879

Gnomad4 SAS AF: 0.783

Gnomad4 FIN AF: 0.888

Gnomad4 NFE AF: 0.836

Gnomad4 OTH AF: 0.852

Alfa AF: 0.840 Hom.: 70972

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1174943; hg19: chr7-22007118;