7-46871342-T-G

Variant names:

• chr7-46871342-T-G
• rs4637723

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.385 in 152,034 control chromosomes in the GnomAD database, including 11,357 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 0.39 (11357 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.42 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: 0.385 AC: 58489 AN: 151916 Hom.: 11349 Cov.: 32

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.385 AC: 58539 AN: 152034 Hom.: 11357 Cov.: 32 AF XY: 0.384 AC XY: 28572 AN XY: 74340

African (AFR) AF: 0.414 AC: 17170 AN: 41452

American (AMR) AF: 0.386 AC: 5901 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1336 AN: 3472

East Asian (EAS) AF: 0.220 AC: 1136 AN: 5172

South Asian (SAS) AF: 0.435 AC: 2098 AN: 4820

European-Finnish (FIN) AF: 0.393 AC: 4155 AN: 10568

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.376 AC: 25570 AN: 67960

Other (OTH) AF: 0.385 AC: 814 AN: 2114

Alfa AF: 0.290 Hom.: 1038

Bravo AF: 0.383

Asia WGS AF: 0.328 AC: 1146 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	0.42
DANN	Benign	0.48
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs4637723; hg19: chr7-46910940;