rs2967017

chr5-19327894-T-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;