5-172724078-A-G

Variant names:

• chr5-172724078-A-G
• rs2618346

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 0.904 in 152,234 control chromosomes in the GnomAD database, including 62,539 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 0.90 (62539 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.211
• Publications: 2 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 (AFR) allele frequency at 95% confidence interval = 0.961 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: 0.904 AC: 137557 AN: 152116 Hom.: 62490 Cov.: 31

Gnomad AFR AF: 0.970

Gnomad AMI AF: 0.947

Gnomad AMR AF: 0.812

Gnomad ASJ AF: 0.913

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.887

Gnomad FIN AF: 0.869

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.902

Gnomad OTH AF: 0.912

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

GnomAD4 genome AF: 0.904 AC: 137662 AN: 152234 Hom.: 62539 Cov.: 31 AF XY: 0.899 AC XY: 66931 AN XY: 74428

African (AFR) AF: 0.969 AC: 40277 AN: 41548

American (AMR) AF: 0.812 AC: 12416 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.913 AC: 3169 AN: 3472

East Asian (EAS) AF: 0.751 AC: 3882 AN: 5168

South Asian (SAS) AF: 0.886 AC: 4265 AN: 4814

European-Finnish (FIN) AF: 0.869 AC: 9209 AN: 10592

Middle Eastern (MID) AF: 0.939 AC: 276 AN: 294

European-Non Finnish (NFE) AF: 0.902 AC: 61377 AN: 68034

Other (OTH) AF: 0.912 AC: 1927 AN: 2114

Alfa AF: 0.887 Hom.: 6935

Bravo AF: 0.902

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.6
DANN	Benign	0.42
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs2618346; hg19: chr5-172151081;