7-3128117-A-G

Variant names:

• chr7-3128117-A-G
• rs6942973

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 0.128 in 152,172 control chromosomes in the GnomAD database, including 2,380 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 0.13 (2380 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.270

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.324 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: 0.128 AC: 19422 AN: 152054 Hom.: 2373 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0563

Gnomad ASJ AF: 0.0524

Gnomad EAS AF: 0.00346

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0305

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0538

Gnomad OTH AF: 0.0906

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

GnomAD4 genome AF: 0.128 AC: 19473 AN: 152172 Hom.: 2380 Cov.: 32 AF XY: 0.125 AC XY: 9267 AN XY: 74420

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.0562

Gnomad4 ASJ AF: 0.0524

Gnomad4 EAS AF: 0.00347

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.0305

Gnomad4 NFE AF: 0.0538

Gnomad4 OTH AF: 0.0925

Alfa AF: 0.0574 Hom.: 824

Bravo AF: 0.136

Asia WGS AF: 0.109 AC: 378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.2
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6942973; hg19: chr7-3167751;