4-110238764-T-A

Variant names:

• chr4-110238764-T-A
• rs12512353

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 0.408 in 151,886 control chromosomes in the GnomAD database, including 13,948 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 0.41 (13948 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.216

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 = 0.632 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: 0.408 AC: 61946 AN: 151768 Hom.: 13944 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.408 AC: 61967 AN: 151886 Hom.: 13948 Cov.: 32 AF XY: 0.410 AC XY: 30412 AN XY: 74200

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.544

Gnomad4 ASJ AF: 0.395

Gnomad4 EAS AF: 0.650

Gnomad4 SAS AF: 0.435

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.468

Gnomad4 OTH AF: 0.401

Alfa AF: 0.428 Hom.: 1857

Bravo AF: 0.409

Asia WGS AF: 0.499 AC: 1735 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
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: rs12512353; hg19: chr4-111159920;