rs2972345

Variant names:

• chr5-121928013-G-C
• rs2972345

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 0.72 in 152,024 control chromosomes in the GnomAD database, including 40,218 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 0.72 (40218 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.918 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: 0.720 AC: 109377 AN: 151906 Hom.: 40200 Cov.: 31

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.765

Gnomad EAS AF: 0.940

Gnomad SAS AF: 0.815

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.755

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.720 AC: 109438 AN: 152024 Hom.: 40218 Cov.: 31 AF XY: 0.727 AC XY: 54014 AN XY: 74324

Gnomad4 AFR AF: 0.568

Gnomad4 AMR AF: 0.791

Gnomad4 ASJ AF: 0.765

Gnomad4 EAS AF: 0.940

Gnomad4 SAS AF: 0.815

Gnomad4 FIN AF: 0.809

Gnomad4 NFE AF: 0.755

Gnomad4 OTH AF: 0.733

Alfa AF: 0.732 Hom.: 5071

Bravo AF: 0.713

Asia WGS AF: 0.875 AC: 3042 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.83
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: rs2972345; hg19: chr5-121263708; COSMIC: COSV60191200;