rs1458149

Variant names:

• chr4-162769196-T-C
• rs1458149
• ENST00000661387.1:n.165+27417T>C

Variant summary

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

The ENST00000661387.1(ENSG00000248431):​n.165+27417T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 150,682 control chromosomes in the GnomAD database, including 8,340 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 0.30 (8340 hom., cov: 28)
• Consequence: ENSG00000248431 ENST00000661387.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.430
• Publications: 3 publications found

Genes affected

ENSG00000248431 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.718 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000661387.1. 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
	ENSG00000248431	ENST00000661387.1		n.165+27417T>C		intron	N/A
	ENSG00000248431	ENST00000728266.1		n.185+27417T>C		intron	N/A
	ENSG00000248431	ENST00000728267.1		n.536-16069T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45037 AN: 150578 Hom.: 8343 Cov.: 28

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.299 AC: 45028 AN: 150682 Hom.: 8340 Cov.: 28 AF XY: 0.310 AC XY: 22759 AN XY: 73502

African (AFR) AF: 0.134 AC: 5495 AN: 41046

American (AMR) AF: 0.497 AC: 7492 AN: 15064

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1394 AN: 3464

East Asian (EAS) AF: 0.738 AC: 3770 AN: 5110

South Asian (SAS) AF: 0.356 AC: 1697 AN: 4764

European-Finnish (FIN) AF: 0.352 AC: 3601 AN: 10220

Middle Eastern (MID) AF: 0.317 AC: 92 AN: 290

European-Non Finnish (NFE) AF: 0.302 AC: 20425 AN: 67732

Other (OTH) AF: 0.341 AC: 709 AN: 2082

Alfa AF: 0.299 Hom.: 994

Bravo AF: 0.304

Asia WGS AF: 0.492 AC: 1709 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.9
DANN	Benign	0.28
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs1458149; hg19: chr4-163690348;