rs1496497

Variant names:

• chr7-45901444-T-G
• rs1496497

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 0.18 in 152,142 control chromosomes in the GnomAD database, including 2,488 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 0.18 (2488 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.579
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.185 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: 0.180 AC: 27347 AN: 152024 Hom.: 2480 Cov.: 33

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.0813

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.0925

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.180 AC: 27384 AN: 152142 Hom.: 2488 Cov.: 33 AF XY: 0.179 AC XY: 13318 AN XY: 74362

African (AFR) AF: 0.187 AC: 7751 AN: 41510

American (AMR) AF: 0.144 AC: 2201 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 778 AN: 3468

East Asian (EAS) AF: 0.195 AC: 1010 AN: 5176

South Asian (SAS) AF: 0.0921 AC: 444 AN: 4820

European-Finnish (FIN) AF: 0.221 AC: 2341 AN: 10574

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12397 AN: 67978

Other (OTH) AF: 0.175 AC: 370 AN: 2112

Alfa AF: 0.194 Hom.: 386

Bravo AF: 0.179

Asia WGS AF: 0.138 AC: 480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.2
DANN	Benign	0.70
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs1496497; hg19: chr7-45941043;