rs3757552

Positions:

• chr7-121323911-A-G
• chr7-121323911-A-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.103 in 152,258 control chromosomes in the GnomAD database, including 1,195 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 0.10 (1195 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.346 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: 0.103 AC: 15608 AN: 152140 Hom.: 1193 Cov.: 32

Gnomad AFR AF: 0.0249

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.0898

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.103 AC: 15615 AN: 152258 Hom.: 1195 Cov.: 32 AF XY: 0.105 AC XY: 7837 AN XY: 74452

Gnomad4 AFR AF: 0.0249

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.359

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.0898

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.116

Alfa AF: 0.111 Hom.: 1490

Bravo AF: 0.104

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	12
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3757552; hg19: chr7-120963965;