rs6537296

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.476 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.328-150804T>C		intron	N/A	ENSP00000497507.1	A0A3B3ISY7
	ENSG00000285783	ENST00000650526.1		n.223-150804T>C		intron	N/A

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

African (AFR) AF: 0.261 AC: 10845 AN: 41500

American (AMR) AF: 0.321 AC: 4904 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1257 AN: 3472

East Asian (EAS) AF: 0.301 AC: 1557 AN: 5180

South Asian (SAS) AF: 0.492 AC: 2370 AN: 4816

European-Finnish (FIN) AF: 0.536 AC: 5641 AN: 10528

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.413 AC: 28060 AN: 67956

Other (OTH) AF: 0.339 AC: 716 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.80
DANN	Benign	0.55
PhyloP100		0.31

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: rs6537296;

hg19: chr4-145487934;