rs267735

chr1-150976020-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 0.412 in 149,772 control chromosomes in the GnomAD database, including 14,452 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 0.41 (14452 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.49

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.536 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: 0.412 AC: 61719 AN: 149676 Hom.: 14456 Cov.: 31

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.429

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.412 AC: 61720 AN: 149772 Hom.: 14452 Cov.: 31 AF XY: 0.410 AC XY: 29969 AN XY: 73110

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.416

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.561

Gnomad4 NFE AF: 0.541

Gnomad4 OTH AF: 0.437

Alfa AF: 0.468 Hom.: 2267

Bravo AF: 0.386

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.018
Dann	Benign	0.12

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs267735; hg19: chr1-150948496;