rs2967017

Variant names:

• chr5-19327894-T-G
• rs2967017

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 0.499 in 151,978 control chromosomes in the GnomAD database, including 19,373 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 0.50 (19373 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.553 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: 0.499 AC: 75760 AN: 151860 Hom.: 19363 Cov.: 32

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.499 AC: 75803 AN: 151978 Hom.: 19373 Cov.: 32 AF XY: 0.500 AC XY: 37128 AN XY: 74296

Gnomad4 AFR AF: 0.446

Gnomad4 AMR AF: 0.562

Gnomad4 ASJ AF: 0.510

Gnomad4 EAS AF: 0.224

Gnomad4 SAS AF: 0.530

Gnomad4 FIN AF: 0.543

Gnomad4 NFE AF: 0.527

Gnomad4 OTH AF: 0.492

Alfa AF: 0.524 Hom.: 32595

Bravo AF: 0.493

Asia WGS AF: 0.409 AC: 1419 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.8
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2967017; hg19: chr5-19328003;