rs1496495

Variant names:

• chr7-45897662-T-C
• rs1496495

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.0882

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.224

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.0915

Gnomad4 FIN AF: 0.220

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.155

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1496495; hg19: chr7-45937261;