6-2355441-C-T

Variant names:

• chr6-2355441-C-T
• rs2505675
• ENST00000657544.1:n.1528G>A

Variant summary

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

The ENST00000657544.1(ENSG00000286512):​n.1528G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 152,000 control chromosomes in the GnomAD database, including 12,960 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 0.40 (12960 hom., cov: 32)
• Consequence: ENSG00000286512 ENST00000657544.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164
• Publications: 11 publications found

Genes affected

ENSG00000286512 (HGNC:):

GMDS-DT (HGNC:48993): (GMDS divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000657544.1. 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
	GMDS-DT	NR_046229.1		n.402+26109C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286512	ENST00000657544.1		n.1528G>A		non_coding_transcript_exon	Exon 3 of 3
	GMDS-DT	ENST00000524770.6	TSL:3	n.440-41780C>T		intron	N/A
	GMDS-DT	ENST00000529893.6	TSL:5	n.374-41780C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60861 AN: 151882 Hom.: 12922 Cov.: 32

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.401 AC: 60953 AN: 152000 Hom.: 12960 Cov.: 32 AF XY: 0.406 AC XY: 30172 AN XY: 74270

African (AFR) AF: 0.520 AC: 21570 AN: 41442

American (AMR) AF: 0.465 AC: 7092 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1266 AN: 3472

East Asian (EAS) AF: 0.575 AC: 2966 AN: 5154

South Asian (SAS) AF: 0.382 AC: 1839 AN: 4818

European-Finnish (FIN) AF: 0.335 AC: 3536 AN: 10554

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21391 AN: 67984

Other (OTH) AF: 0.391 AC: 825 AN: 2110

Alfa AF: 0.351 Hom.: 34753

Bravo AF: 0.415

Asia WGS AF: 0.501 AC: 1746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.53
PhyloP100		-0.16

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: rs2505675;

hg19: chr6-2355675;