rs2995073

Positions:

• chr1-167557341-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 0.429 in 151,440 control chromosomes in the GnomAD database, including 14,092 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 0.43 (14092 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100

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 (AFR) allele frequency at 95% confidence interval = 0.478 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: 0.429 AC: 64918 AN: 151324 Hom.: 14092 Cov.: 30

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.429 AC: 64937 AN: 151440 Hom.: 14092 Cov.: 30 AF XY: 0.424 AC XY: 31371 AN XY: 74008

Gnomad4 AFR AF: 0.484

Gnomad4 AMR AF: 0.474

Gnomad4 ASJ AF: 0.451

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.353

Gnomad4 NFE AF: 0.412

Gnomad4 OTH AF: 0.443

Alfa AF: 0.422 Hom.: 1643

Bravo AF: 0.446

Asia WGS AF: 0.313 AC: 1089 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	6.4
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2995073; hg19: chr1-167526578;