rs1496495

Variant names:

• chr7-45897662-T-C
• rs1496495

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 0.152 in 152,148 control chromosomes in the GnomAD database, including 1,893 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 0.15 (1893 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.441
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• 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: 0.151 AC: 23031 AN: 152030 Hom.: 1889 Cov.: 32

Gnomad AFR AF: 0.0879

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.0916

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.152 AC: 23062 AN: 152148 Hom.: 1893 Cov.: 32 AF XY: 0.152 AC XY: 11292 AN XY: 74402

African (AFR) AF: 0.0882 AC: 3664 AN: 41520

American (AMR) AF: 0.134 AC: 2054 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 778 AN: 3470

East Asian (EAS) AF: 0.195 AC: 1011 AN: 5186

South Asian (SAS) AF: 0.0915 AC: 441 AN: 4822

European-Finnish (FIN) AF: 0.220 AC: 2326 AN: 10568

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12369 AN: 67982

Other (OTH) AF: 0.155 AC: 328 AN: 2112

Alfa AF: 0.176 Hom.: 303

Bravo AF: 0.146

Asia WGS AF: 0.132 AC: 459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	12
DANN	Benign	0.96
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs1496495; hg19: chr7-45937261;