rs4959677

Variant names:

• chr6-2500586-G-C
• rs4959677
• ENST00000659523.1:n.621+19417G>C

Your query was ambiguous. Multiple possible variants found:

• chr6-2500586-G-C
• chr6-2500586-G-T

Variant summary

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

The ENST00000659523.1(GMDS-DT):​n.621+19417G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 152,104 control chromosomes in the GnomAD database, including 14,584 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 0.42 (14584 hom., cov: 32)
• Consequence: GMDS-DT ENST00000659523.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.237
• Publications: 15 publications found

Genes affected

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

ENSG00000300829 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000659523.1. 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
	GMDS-DT	ENST00000659523.1		n.621+19417G>C		intron	N/A
	ENSG00000300829	ENST00000774283.1		n.645+1221C>G		intron	N/A
	ENSG00000300829	ENST00000774284.1		n.675+1221C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64430 AN: 151986 Hom.: 14585 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.424 AC: 64455 AN: 152104 Hom.: 14584 Cov.: 32 AF XY: 0.426 AC XY: 31647 AN XY: 74352

African (AFR) AF: 0.275 AC: 11397 AN: 41470

American (AMR) AF: 0.509 AC: 7775 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.538 AC: 1867 AN: 3472

East Asian (EAS) AF: 0.216 AC: 1120 AN: 5182

South Asian (SAS) AF: 0.461 AC: 2227 AN: 4828

European-Finnish (FIN) AF: 0.488 AC: 5151 AN: 10566

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.490 AC: 33294 AN: 68002

Other (OTH) AF: 0.456 AC: 963 AN: 2110

Alfa AF: 0.432 Hom.: 1790

Bravo AF: 0.420

Asia WGS AF: 0.345 AC: 1203 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	13
DANN	Benign	0.55
PhyloP100		0.24

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: rs4959677;

hg19: chr6-2500820;