4-20174612-C-T

Variant names:

• chr4-20174612-C-T
• rs1436293

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 0.863 in 152,054 control chromosomes in the GnomAD database, including 56,622 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 0.86 (56622 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.29
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.951 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: 0.863 AC: 131077 AN: 151936 Hom.: 56582 Cov.: 30

Gnomad AFR AF: 0.862

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.901

Gnomad ASJ AF: 0.909

Gnomad EAS AF: 0.974

Gnomad SAS AF: 0.868

Gnomad FIN AF: 0.862

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.845

Gnomad OTH AF: 0.882

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

GnomAD4 genome AF: 0.863 AC: 131174 AN: 152054 Hom.: 56622 Cov.: 30 AF XY: 0.865 AC XY: 64266 AN XY: 74320

African (AFR) AF: 0.862 AC: 35739 AN: 41470

American (AMR) AF: 0.901 AC: 13759 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.909 AC: 3156 AN: 3472

East Asian (EAS) AF: 0.974 AC: 5027 AN: 5162

South Asian (SAS) AF: 0.867 AC: 4179 AN: 4820

European-Finnish (FIN) AF: 0.862 AC: 9110 AN: 10564

Middle Eastern (MID) AF: 0.905 AC: 266 AN: 294

European-Non Finnish (NFE) AF: 0.845 AC: 57451 AN: 67978

Other (OTH) AF: 0.884 AC: 1863 AN: 2108

Alfa AF: 0.862 Hom.: 8738

Bravo AF: 0.868

Asia WGS AF: 0.918 AC: 3186 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.12
DANN	Benign	0.24
PhyloP100		-3.3

Splicing

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

Other links and lift over

dbSNP: rs1436293; hg19: chr4-20176235;