5-118647917-C-A

Variant names:

• chr5-118647917-C-A
• rs2972219

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 0.801 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.946 AC: 39269 AN: 41526

American (AMR) AF: 0.747 AC: 11415 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.764 AC: 2651 AN: 3470

East Asian (EAS) AF: 0.968 AC: 5019 AN: 5186

South Asian (SAS) AF: 0.802 AC: 3864 AN: 4816

European-Finnish (FIN) AF: 0.746 AC: 7881 AN: 10562

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.721 AC: 49036 AN: 67980

Other (OTH) AF: 0.780 AC: 1649 AN: 2114

Alfa AF: 0.746 Hom.: 188150

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
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs2972219; hg19: chr5-117983612;