rs1458149

Positions:

• chr4-162769196-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000661387.1(ENSG00000248431):​n.165+27417T>C variant causes a intron, non coding transcript 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: ENST00000661387.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.430

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000661387.1	n.165+27417T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.497

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.738

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.352

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.341

Alfa AF: 0.306 Hom.: 987

Bravo AF: 0.304

Asia WGS AF: 0.492 AC: 1709 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1458149; hg19: chr4-163690348;