rs1398244

chr4-144641305-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 0.293 in 152,032 control chromosomes in the GnomAD database, including 7,099 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 0.29 (7099 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.37 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: 0.293 AC: 44460 AN: 151914 Hom.: 7101 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.293 AC: 44474 AN: 152032 Hom.: 7099 Cov.: 32 AF XY: 0.285 AC XY: 21178 AN XY: 74288

Gnomad4 AFR AF: 0.189

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.327

Gnomad4 NFE AF: 0.374

Gnomad4 OTH AF: 0.299

Alfa AF: 0.350 Hom.: 19511

Bravo AF: 0.283

Asia WGS AF: 0.161 AC: 561 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.11
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1398244; hg19: chr4-145562457;