rs67631072

Positions:

• chr1-37996149-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.42 in 152,098 control chromosomes in the GnomAD database, including 15,649 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 0.42 (15649 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.87

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63957 AN: 151984 Hom.: 15653 Cov.: 34

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.579

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.420 AC: 63951 AN: 152098 Hom.: 15649 Cov.: 34 AF XY: 0.422 AC XY: 31397 AN XY: 74354

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.492

Gnomad4 EAS AF: 0.344

Gnomad4 SAS AF: 0.437

Gnomad4 FIN AF: 0.579

Gnomad4 NFE AF: 0.552

Gnomad4 OTH AF: 0.435

Alfa AF: 0.490 Hom.: 2485

Bravo AF: 0.393

Asia WGS AF: 0.404 AC: 1405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	20
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs67631072; hg19: chr1-38461821;