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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.805

Gnomad4 AMR AF: 0.769

Gnomad4 ASJ AF: 0.663

Gnomad4 EAS AF: 0.936

Gnomad4 SAS AF: 0.778

Gnomad4 FIN AF: 0.710

Gnomad4 NFE AF: 0.711

Gnomad4 OTH AF: 0.730

Alfa AF: 0.711 Hom.: 49235

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

Splicing

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

Publications

LitVar

Other links and lift over

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