rs2995073

Variant names:

• chr1-167557341-C-T
• rs2995073

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;