4-110793263-T-G

Variant names:

• chr4-110793263-T-G
• rs13143308

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 0.704 in 151,978 control chromosomes in the GnomAD database, including 38,555 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 0.70 (38555 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.765 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: 0.704 AC: 106892 AN: 151858 Hom.: 38527 Cov.: 32

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.922

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.771

Gnomad OTH AF: 0.708

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

GnomAD4 genome AF: 0.704 AC: 106968 AN: 151978 Hom.: 38555 Cov.: 32 AF XY: 0.688 AC XY: 51116 AN XY: 74274

Gnomad4 AFR AF: 0.702

Gnomad4 AMR AF: 0.593

Gnomad4 ASJ AF: 0.622

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.660

Gnomad4 FIN AF: 0.679

Gnomad4 NFE AF: 0.771

Gnomad4 OTH AF: 0.706

Alfa AF: 0.760 Hom.: 36514

Bravo AF: 0.700

Asia WGS AF: 0.501 AC: 1744 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.32
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13143308; hg19: chr4-111714419;