5-121928013-G-C

Variant names:

• chr5-121928013-G-C
• rs2972345

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.568 AC: 23522 AN: 41418

American (AMR) AF: 0.791 AC: 12074 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.765 AC: 2657 AN: 3472

East Asian (EAS) AF: 0.940 AC: 4867 AN: 5178

South Asian (SAS) AF: 0.815 AC: 3932 AN: 4826

European-Finnish (FIN) AF: 0.809 AC: 8570 AN: 10590

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.755 AC: 51307 AN: 67954

Other (OTH) AF: 0.733 AC: 1549 AN: 2112

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2972345; hg19: chr5-121263708; COSMIC: COSV60191200;