chr4-144566782-A-G

Position:

• chr4-144566782-A-G

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 0.367 in 152,058 control chromosomes in the GnomAD database, including 10,773 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 0.37 (10773 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.309

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55805 AN: 151940 Hom.: 10765 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.367 AC: 55821 AN: 152058 Hom.: 10773 Cov.: 32 AF XY: 0.373 AC XY: 27689 AN XY: 74304

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.301

Gnomad4 SAS AF: 0.492

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.413

Gnomad4 OTH AF: 0.339

Alfa AF: 0.406 Hom.: 1661

Bravo AF: 0.339

Asia WGS AF: 0.367 AC: 1277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.80
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6537296; hg19: chr4-145487934;