4-110238764-T-A

Variant names:

• chr4-110238764-T-A
• rs12512353

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.218 AC: 9044 AN: 41432

American (AMR) AF: 0.544 AC: 8294 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1367 AN: 3462

East Asian (EAS) AF: 0.650 AC: 3350 AN: 5150

South Asian (SAS) AF: 0.435 AC: 2091 AN: 4802

European-Finnish (FIN) AF: 0.448 AC: 4714 AN: 10522

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.468 AC: 31774 AN: 67950

Other (OTH) AF: 0.401 AC: 847 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.43
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs12512353; hg19: chr4-111159920;