4-180716762-A-G

Variant names:

• chr4-180716762-A-G
• rs2545308

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 0.616 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.510

Gnomad4 AMR AF: 0.705

Gnomad4 ASJ AF: 0.595

Gnomad4 EAS AF: 0.816

Gnomad4 SAS AF: 0.684

Gnomad4 FIN AF: 0.682

Gnomad4 NFE AF: 0.631

Gnomad4 OTH AF: 0.626

Alfa AF: 0.630 Hom.: 28465

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2545308; hg19: chr4-181637915;