rs12512353

chr4-110238764-T-Achr4-110238764-T-Cchr4-110238764-T-G

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/exons	MANE	UniProt

Ensembl

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