rs344971

Variant names:

• chr3-145360822-A-G
• rs344971

Your query was ambiguous. Multiple possible variants found:

• chr3-145360822-A-G
• chr3-145360822-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 0.923 in 151,916 control chromosomes in the GnomAD database, including 64,768 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 0.92 (64768 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.952 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: 0.923 AC: 140131 AN: 151798 Hom.: 64712 Cov.: 32

Gnomad AFR AF: 0.960

Gnomad AMI AF: 0.891

Gnomad AMR AF: 0.884

Gnomad ASJ AF: 0.904

Gnomad EAS AF: 0.956

Gnomad SAS AF: 0.915

Gnomad FIN AF: 0.926

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.908

Gnomad OTH AF: 0.919

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

GnomAD4 genome AF: 0.923 AC: 140245 AN: 151916 Hom.: 64768 Cov.: 32 AF XY: 0.923 AC XY: 68503 AN XY: 74240

Gnomad4 AFR AF: 0.960

Gnomad4 AMR AF: 0.885

Gnomad4 ASJ AF: 0.904

Gnomad4 EAS AF: 0.956

Gnomad4 SAS AF: 0.916

Gnomad4 FIN AF: 0.926

Gnomad4 NFE AF: 0.909

Gnomad4 OTH AF: 0.919

Alfa AF: 0.911 Hom.: 12315

Bravo AF: 0.920

Asia WGS AF: 0.932 AC: 3232 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.61
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs344971; hg19: chr3-145078609;