rs957523

Positions:

• chr7-114709601-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;