7-3128117-A-G

Position:

• chr7-3128117-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;