chr4-109902959-G-A

Position:

• chr4-109902959-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;