rs6537296

Variant names:

• chr4-144566782-A-G
• rs6537296
• ENST00000649263.1:n.328-150804T>C

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.328-150804T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.309

Genes affected

ENSG00000285713 (HGNC:):

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285713	ENST00000649263.1	n.328-150804T>C		intron_variant	Intron 4 of 8			ENSP00000497507.1
ENSG00000285783	ENST00000650526.1	n.223-150804T>C		intron_variant	Intron 2 of 14

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;