rs1497960

Variant names:

• chr4-166158004-C-T
• rs1497960

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 0.0551 in 152,226 control chromosomes in the GnomAD database, including 241 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 0.055 (241 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.835
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0675 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: 0.0552 AC: 8389 AN: 152108 Hom.: 241 Cov.: 33

Gnomad AFR AF: 0.0352

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0711

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.0390

Gnomad SAS AF: 0.0553

Gnomad FIN AF: 0.0361

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0652

Gnomad OTH AF: 0.0752

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

GnomAD4 genome AF: 0.0551 AC: 8391 AN: 152226 Hom.: 241 Cov.: 33 AF XY: 0.0546 AC XY: 4061 AN XY: 74434

African (AFR) AF: 0.0352 AC: 1462 AN: 41546

American (AMR) AF: 0.0710 AC: 1086 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 353 AN: 3468

East Asian (EAS) AF: 0.0393 AC: 203 AN: 5164

South Asian (SAS) AF: 0.0559 AC: 270 AN: 4828

European-Finnish (FIN) AF: 0.0361 AC: 383 AN: 10598

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0651 AC: 4430 AN: 68014

Other (OTH) AF: 0.0744 AC: 157 AN: 2110

Alfa AF: 0.0182 Hom.: 10

Bravo AF: 0.0578

Asia WGS AF: 0.0640 AC: 222 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.86
DANN	Benign	0.21
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs1497960; hg19: chr4-167079156;