rs2972219

chr5-118647917-C-Achr5-118647917-C-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 0.801 in 152,144 control chromosomes in the GnomAD database, including 49,592 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 0.80 (49592 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.384

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.945 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: 0.800 AC: 121690 AN: 152024 Hom.: 49528 Cov.: 32

Gnomad AFR AF: 0.946

Gnomad AMI AF: 0.891

Gnomad AMR AF: 0.746

Gnomad ASJ AF: 0.764

Gnomad EAS AF: 0.968

Gnomad SAS AF: 0.801

Gnomad FIN AF: 0.746

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.721

Gnomad OTH AF: 0.778

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

GnomAD4 genome AF: 0.801 AC: 121820 AN: 152144 Hom.: 49592 Cov.: 32 AF XY: 0.801 AC XY: 59602 AN XY: 74372

Gnomad4 AFR AF: 0.946

Gnomad4 AMR AF: 0.747

Gnomad4 ASJ AF: 0.764

Gnomad4 EAS AF: 0.968

Gnomad4 SAS AF: 0.802

Gnomad4 FIN AF: 0.746

Gnomad4 NFE AF: 0.721

Gnomad4 OTH AF: 0.780

Alfa AF: 0.734 Hom.: 81827

Bravo AF: 0.809

Asia WGS AF: 0.864 AC: 3005 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	3.7
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2972219; hg19: chr5-117983612;