rs3019164

Variant names:

• chr8-103019513-A-C
• rs3019164

Your query was ambiguous. Multiple possible variants found:

• chr8-103019513-A-C
• chr8-103019513-A-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 0.129 in 151,676 control chromosomes in the GnomAD database, including 2,726 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 0.13 (2726 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.344 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: 0.129 AC: 19487 AN: 151558 Hom.: 2718 Cov.: 31

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0809

Gnomad ASJ AF: 0.0331

Gnomad EAS AF: 0.0471

Gnomad SAS AF: 0.0244

Gnomad FIN AF: 0.0191

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0434

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.129 AC: 19518 AN: 151676 Hom.: 2726 Cov.: 31 AF XY: 0.124 AC XY: 9193 AN XY: 74120

Gnomad4 AFR AF: 0.348

Gnomad4 AMR AF: 0.0807

Gnomad4 ASJ AF: 0.0331

Gnomad4 EAS AF: 0.0470

Gnomad4 SAS AF: 0.0238

Gnomad4 FIN AF: 0.0191

Gnomad4 NFE AF: 0.0433

Gnomad4 OTH AF: 0.112

Alfa AF: 0.0325 Hom.: 52

Bravo AF: 0.143

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3019164; hg19: chr8-104031741;