rs9660548

chr1-37860565-T-A

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 0.121 in 152,322 control chromosomes in the GnomAD database, including 1,328 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 0.12 (1328 hom., cov: 33)
  • Exomes 𝑓: 0.14 (0 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.155 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: 0.121 AC: 18462 AN: 152168 Hom.: 1326 Cov.: 33

Gnomad AFR AF: 0.0503

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.0596

Gnomad EAS AF: 0.0816

Gnomad SAS AF: 0.0990

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.118

GnomAD4 exome AF: 0.139 AC: 5 AN: 36 Hom.: 0 AF XY: 0.115 AC XY: 3 AN XY: 26

Gnomad4 FIN exome AF: 0.167

Gnomad4 NFE exome AF: 0.115

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.121 AC: 18464 AN: 152286 Hom.: 1328 Cov.: 33 AF XY: 0.122 AC XY: 9102 AN XY: 74450

Gnomad4 AFR AF: 0.0502

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.0596

Gnomad4 EAS AF: 0.0814

Gnomad4 SAS AF: 0.0995

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.116

Alfa AF: 0.137 Hom.: 175

Bravo AF: 0.113

Asia WGS AF: 0.0980 AC: 340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	6.9
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9660548; hg19: chr1-38326237; COSMIC: COSV65959959;