rs4730276

chr7-107843992-G-Achr7-107843992-G-T

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 0.324 in 151,832 control chromosomes in the GnomAD database, including 8,730 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 0.32 (8730 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.368

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49129 AN: 151716 Hom.: 8723 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.324 AC: 49151 AN: 151832 Hom.: 8730 Cov.: 32 AF XY: 0.324 AC XY: 24040 AN XY: 74194

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.372

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.430

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.325

Alfa AF: 0.374 Hom.: 24728

Bravo AF: 0.311

Asia WGS AF: 0.318 AC: 1105 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.80
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4730276; hg19: chr7-107484437; COSMIC: COSV56009164;