7-49594206-A-G

Variant names:

• chr7-49594206-A-G
• rs4492324

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 0.276 in 147,750 control chromosomes in the GnomAD database, including 6,937 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 0.28 (6937 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.746
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.373 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: 0.276 AC: 40743 AN: 147632 Hom.: 6942 Cov.: 33

Gnomad AFR AF: 0.0739

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.276 AC: 40717 AN: 147750 Hom.: 6937 Cov.: 33 AF XY: 0.274 AC XY: 19721 AN XY: 71910

African (AFR) AF: 0.0736 AC: 2875 AN: 39042

American (AMR) AF: 0.298 AC: 4371 AN: 14670

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1585 AN: 3452

East Asian (EAS) AF: 0.163 AC: 806 AN: 4954

South Asian (SAS) AF: 0.203 AC: 910 AN: 4486

European-Finnish (FIN) AF: 0.343 AC: 3539 AN: 10312

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.377 AC: 25448 AN: 67574

Other (OTH) AF: 0.322 AC: 663 AN: 2060

Alfa AF: 0.327 Hom.: 14365

Bravo AF: 0.257

Asia WGS AF: 0.178 AC: 620 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.2
DANN	Benign	0.55
PhyloP100		0.75

Splicing

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

Other links and lift over

dbSNP: rs4492324; hg19: chr7-49633802;