rs957523

Variant names:

• chr7-114709601-T-C
• rs957523

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 0.162 in 152,122 control chromosomes in the GnomAD database, including 3,696 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 0.16 (3696 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.377 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: 0.161 AC: 24534 AN: 152002 Hom.: 3688 Cov.: 32

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.0295

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.0433

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.162 AC: 24583 AN: 152122 Hom.: 3696 Cov.: 32 AF XY: 0.162 AC XY: 12064 AN XY: 74380

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.352

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.0295

Gnomad4 NFE AF: 0.0433

Gnomad4 OTH AF: 0.168

Alfa AF: 0.0121 Hom.: 8

Bravo AF: 0.180

Asia WGS AF: 0.250 AC: 868 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.7
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs957523; hg19: chr7-114349656;