rs2343278

chr1-162968913-G-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 0.686 in 152,018 control chromosomes in the GnomAD database, including 36,200 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 0.69 (36200 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.332

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 (AFR) allele frequency at 95% confidence interval = 0.778 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: 0.686 AC: 104171 AN: 151900 Hom.: 36135 Cov.: 31

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.643

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.686 AC: 104302 AN: 152018 Hom.: 36200 Cov.: 31 AF XY: 0.685 AC XY: 50894 AN XY: 74280

Gnomad4 AFR AF: 0.785

Gnomad4 AMR AF: 0.718

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.719

Gnomad4 SAS AF: 0.527

Gnomad4 FIN AF: 0.626

Gnomad4 NFE AF: 0.643

Gnomad4 OTH AF: 0.688

Alfa AF: 0.655 Hom.: 46586

Bravo AF: 0.700

Asia WGS AF: 0.651 AC: 2263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.058
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2343278; hg19: chr1-162938703;