chr7-46537458-A-G

Variant names:

• chr7-46537458-A-G
• rs723149

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 0.65 in 152,200 control chromosomes in the GnomAD database, including 34,126 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 0.65 (34126 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.321
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.888 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: 0.650 AC: 98800 AN: 152084 Hom.: 34064 Cov.: 33

Gnomad AFR AF: 0.896

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.692

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.650 AC: 98917 AN: 152200 Hom.: 34126 Cov.: 33 AF XY: 0.646 AC XY: 48054 AN XY: 74402

African (AFR) AF: 0.896 AC: 37221 AN: 41542

American (AMR) AF: 0.495 AC: 7565 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1846 AN: 3470

East Asian (EAS) AF: 0.700 AC: 3617 AN: 5170

South Asian (SAS) AF: 0.691 AC: 3337 AN: 4830

European-Finnish (FIN) AF: 0.539 AC: 5701 AN: 10584

Middle Eastern (MID) AF: 0.479 AC: 140 AN: 292

European-Non Finnish (NFE) AF: 0.555 AC: 37734 AN: 68000

Other (OTH) AF: 0.624 AC: 1319 AN: 2114

Alfa AF: 0.575 Hom.: 44782

Bravo AF: 0.653

Asia WGS AF: 0.733 AC: 2548 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.6
DANN	Benign	0.84
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs723149; hg19: chr7-46577056;