6-2485574-A-G

Variant names:

• chr6-2485574-A-G
• rs6911560
• ENST00000670895.1:n.4399A>G

Variant summary

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

The ENST00000670895.1(GMDS-DT):​n.4399A>G 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 0.073 in 152,304 control chromosomes in the GnomAD database, including 618 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 0.073 (618 hom., cov: 33)
• Consequence: GMDS-DT ENST00000670895.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.42
• Publications: 0 publications found

Genes affected

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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000670895.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GMDS-DT	ENST00000670895.1		n.4399A>G		non_coding_transcript_exon	Exon 5 of 5
	GMDS-DT	ENST00000654526.1		n.970-3105A>G		intron	N/A
	GMDS-DT	ENST00000659523.1		n.621+4405A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0728 AC: 11077 AN: 152186 Hom.: 610 Cov.: 33

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0387

Gnomad ASJ AF: 0.0608

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0440

Gnomad FIN AF: 0.0582

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0385

Gnomad OTH AF: 0.0632

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

GnomAD4 genome AF: 0.0730 AC: 11119 AN: 152304 Hom.: 618 Cov.: 33 AF XY: 0.0735 AC XY: 5477 AN XY: 74472

African (AFR) AF: 0.160 AC: 6656 AN: 41552

American (AMR) AF: 0.0386 AC: 591 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0608 AC: 211 AN: 3472

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5188

South Asian (SAS) AF: 0.0441 AC: 213 AN: 4834

European-Finnish (FIN) AF: 0.0582 AC: 618 AN: 10610

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0385 AC: 2621 AN: 68030

Other (OTH) AF: 0.0625 AC: 132 AN: 2112

Alfa AF: 0.0430 Hom.: 69

Bravo AF: 0.0749

Asia WGS AF: 0.0310 AC: 109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	11
DANN	Benign	0.75
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs6911560; hg19: chr6-2485808;