4-167253544-C-T

Variant names:

• chr4-167253544-C-T
• rs1485318

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 0.145 in 151,628 control chromosomes in the GnomAD database, including 1,837 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 0.15 (1837 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0840
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.246 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: 0.145 AC: 22043 AN: 151500 Hom.: 1837 Cov.: 32

Gnomad AFR AF: 0.0722

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.0938

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.145 AC: 22050 AN: 151628 Hom.: 1837 Cov.: 32 AF XY: 0.147 AC XY: 10879 AN XY: 74086

African (AFR) AF: 0.0721 AC: 2985 AN: 41406

American (AMR) AF: 0.127 AC: 1931 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 633 AN: 3468

East Asian (EAS) AF: 0.0939 AC: 483 AN: 5146

South Asian (SAS) AF: 0.258 AC: 1239 AN: 4806

European-Finnish (FIN) AF: 0.167 AC: 1751 AN: 10514

Middle Eastern (MID) AF: 0.123 AC: 34 AN: 276

European-Non Finnish (NFE) AF: 0.182 AC: 12358 AN: 67796

Other (OTH) AF: 0.154 AC: 324 AN: 2100

Alfa AF: 0.0736 Hom.: 91

Bravo AF: 0.135

Asia WGS AF: 0.140 AC: 480 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.3
DANN	Benign	0.29
PhyloP100		0.084

Splicing

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

Other links and lift over

dbSNP: rs1485318; hg19: chr4-168174695;