4-180716762-A-G

Variant names:

• chr4-180716762-A-G
• rs2545308

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 0.616 in 151,994 control chromosomes in the GnomAD database, including 29,217 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 0.62 (29217 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.236
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.796 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: 0.616 AC: 93536 AN: 151876 Hom.: 29203 Cov.: 32

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.815

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.616 AC: 93588 AN: 151994 Hom.: 29217 Cov.: 32 AF XY: 0.620 AC XY: 46048 AN XY: 74290

African (AFR) AF: 0.510 AC: 21160 AN: 41468

American (AMR) AF: 0.705 AC: 10759 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2063 AN: 3470

East Asian (EAS) AF: 0.816 AC: 4205 AN: 5152

South Asian (SAS) AF: 0.684 AC: 3292 AN: 4814

European-Finnish (FIN) AF: 0.682 AC: 7212 AN: 10574

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.631 AC: 42863 AN: 67934

Other (OTH) AF: 0.626 AC: 1323 AN: 2112

Alfa AF: 0.627 Hom.: 37408

Bravo AF: 0.614

Asia WGS AF: 0.737 AC: 2559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.2
DANN	Benign	0.74
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs2545308; hg19: chr4-181637915;