rs718768

Variant names:

• chr4-109902959-G-A
• rs718768

Your query was ambiguous. Multiple possible variants found:

• chr4-109902959-G-A
• chr4-109902959-G-C

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 0.751 in 152,196 control chromosomes in the GnomAD database, including 43,310 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 0.75 (43310 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.914 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: 0.751 AC: 114212 AN: 152078 Hom.: 43250 Cov.: 33

Gnomad AFR AF: 0.805

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.769

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.778

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.727

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

GnomAD4 genome AF: 0.751 AC: 114334 AN: 152196 Hom.: 43310 Cov.: 33 AF XY: 0.754 AC XY: 56120 AN XY: 74396

African (AFR) AF: 0.805 AC: 33435 AN: 41532

American (AMR) AF: 0.769 AC: 11761 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2298 AN: 3466

East Asian (EAS) AF: 0.936 AC: 4861 AN: 5194

South Asian (SAS) AF: 0.778 AC: 3757 AN: 4826

European-Finnish (FIN) AF: 0.710 AC: 7509 AN: 10572

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.711 AC: 48338 AN: 68002

Other (OTH) AF: 0.730 AC: 1543 AN: 2114

Alfa AF: 0.717 Hom.: 64100

Bravo AF: 0.757

Asia WGS AF: 0.859 AC: 2985 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.43
PhyloP100		0.025

Splicing

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

Other links and lift over

dbSNP: rs718768; hg19: chr4-110824115; COSMIC: COSV69025164;