rs1398244

Variant names:

• chr4-144641305-C-T
• rs1398244
• ENST00000649263.1:n.328-225327G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000649263.1(ENSG00000285713):​n.328-225327G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 7 publications found

Genes affected

ENSG00000285713 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649263.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285713	ENST00000649263.1		n.328-225327G>A		intron	N/A	ENSP00000497507.1	A0A3B3ISY7
	ENSG00000285783	ENST00000650526.1		n.222+113852G>A		intron	N/A

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

African (AFR) AF: 0.189 AC: 7833 AN: 41484

American (AMR) AF: 0.249 AC: 3814 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 1232 AN: 3470

East Asian (EAS) AF: 0.172 AC: 891 AN: 5166

South Asian (SAS) AF: 0.178 AC: 858 AN: 4818

European-Finnish (FIN) AF: 0.327 AC: 3450 AN: 10540

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.374 AC: 25391 AN: 67948

Other (OTH) AF: 0.299 AC: 632 AN: 2112

Alfa AF: 0.342 Hom.: 40251

Bravo AF: 0.283

Asia WGS AF: 0.161 AC: 561 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.11
DANN	Benign	0.66
PhyloP100		-1.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1398244;

hg19: chr4-145562457;