4-110728095-C-T

Position:

• chr4-110728095-C-T

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 0.156 in 152,114 control chromosomes in the GnomAD database, including 2,167 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 0.16 (2167 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23692 AN: 151996 Hom.: 2164 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.0505

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.156 AC: 23718 AN: 152114 Hom.: 2167 Cov.: 32 AF XY: 0.162 AC XY: 12081 AN XY: 74350

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.357

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.173

Alfa AF: 0.166 Hom.: 479

Bravo AF: 0.160

Asia WGS AF: 0.196 AC: 683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.5
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12647316; hg19: chr4-111649251;