rs1497960

chr4-166158004-C-T

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 0.0551 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0352

Gnomad4 AMR AF: 0.0710

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.0393

Gnomad4 SAS AF: 0.0559

Gnomad4 FIN AF: 0.0361

Gnomad4 NFE AF: 0.0651

Gnomad4 OTH AF: 0.0744

Alfa AF: 0.0166 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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1497960; hg19: chr4-167079156;