rs2011345

Variant names:

• chr1-171353382-C-T
• rs2011345

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 0.573 in 152,142 control chromosomes in the GnomAD database, including 27,280 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 0.57 (27280 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.613

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 = 0.839 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: 0.573 AC: 87058 AN: 152024 Hom.: 27231 Cov.: 32

Gnomad AFR AF: 0.846

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.573 AC: 87157 AN: 152142 Hom.: 27280 Cov.: 32 AF XY: 0.573 AC XY: 42593 AN XY: 74372

Gnomad4 AFR AF: 0.846

Gnomad4 AMR AF: 0.464

Gnomad4 ASJ AF: 0.522

Gnomad4 EAS AF: 0.451

Gnomad4 SAS AF: 0.665

Gnomad4 FIN AF: 0.457

Gnomad4 NFE AF: 0.458

Gnomad4 OTH AF: 0.532

Alfa AF: 0.524 Hom.: 3751

Bravo AF: 0.582

Asia WGS AF: 0.545 AC: 1895 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.49
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2011345; hg19: chr1-171322521;