rs2967001

Variant names:

• chr5-19386134-T-C
• rs2967001

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 0.325 in 150,000 control chromosomes in the GnomAD database, including 8,507 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 0.33 (8507 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.107

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.423 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: 0.325 AC: 48745 AN: 149894 Hom.: 8510 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.0924

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.325 AC: 48762 AN: 150000 Hom.: 8507 Cov.: 32 AF XY: 0.325 AC XY: 23808 AN XY: 73354

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.432

Gnomad4 ASJ AF: 0.308

Gnomad4 EAS AF: 0.0920

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.354

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.307

Alfa AF: 0.363 Hom.: 1650

Bravo AF: 0.322

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.2
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2967001; hg19: chr5-19386243;