rs2358944

Variant names:

• chr12-65723778-G-A
• rs2358944

Your query was ambiguous. Multiple possible variants found:

• chr12-65723778-G-A
• chr12-65723778-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.64 in 152,058 control chromosomes in the GnomAD database, including 37,054 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 0.64 (37054 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.90

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.858 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: 0.641 AC: 97341 AN: 151940 Hom.: 37071 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.786

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.904

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.864

Gnomad OTH AF: 0.706

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

GnomAD4 genome AF: 0.640 AC: 97316 AN: 152058 Hom.: 37054 Cov.: 32 AF XY: 0.637 AC XY: 47353 AN XY: 74330

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.645

Gnomad4 ASJ AF: 0.904

Gnomad4 EAS AF: 0.310

Gnomad4 SAS AF: 0.657

Gnomad4 FIN AF: 0.829

Gnomad4 NFE AF: 0.864

Gnomad4 OTH AF: 0.699

Alfa AF: 0.817 Hom.: 112954

Bravo AF: 0.604

Asia WGS AF: 0.437 AC: 1522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	17
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2358944; hg19: chr12-66117558;