4-144567182-C-T

Position:

• chr4-144567182-C-T

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 0.319 in 152,020 control chromosomes in the GnomAD database, including 9,479 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 0.32 (9479 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.287

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 (SAS) allele frequency at 95% confidence interval = 0.475 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: 0.319 AC: 48420 AN: 151902 Hom.: 9470 Cov.: 32

Gnomad AFR AF: 0.0950

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.319 AC: 48432 AN: 152020 Hom.: 9479 Cov.: 32 AF XY: 0.326 AC XY: 24199 AN XY: 74284

Gnomad4 AFR AF: 0.0948

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.300

Gnomad4 SAS AF: 0.492

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.412

Gnomad4 OTH AF: 0.304

Alfa AF: 0.379 Hom.: 1566

Bravo AF: 0.284

Asia WGS AF: 0.360 AC: 1251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	9.5
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1542725; hg19: chr4-145488334;