4-144775888-C-T

Position:

• chr4-144775888-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 0.194 in 152,042 control chromosomes in the GnomAD database, including 3,661 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 0.19 (3661 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.835

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.332 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: 0.194 AC: 29448 AN: 151924 Hom.: 3645 Cov.: 32

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.194 AC: 29528 AN: 152042 Hom.: 3661 Cov.: 32 AF XY: 0.196 AC XY: 14606 AN XY: 74346

Gnomad4 AFR AF: 0.337

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.176

Alfa AF: 0.122 Hom.: 2716

Bravo AF: 0.205

Asia WGS AF: 0.287 AC: 996 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.65
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2353934; hg19: chr4-145697040;