rs3734505

Variant names:

• chr6-2413354-G-A
• rs3734505
• ENST00000505870.5:n.7980G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000505870.5(GMDS-DT):​n.7980G>A variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.136 in 151,482 control chromosomes in the GnomAD database, including 1,544 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 0.14 (1544 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: GMDS-DT ENST00000505870.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.06
• Publications: 6 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GMDS-DT	NR_046229.1	n.1351G>A		non_coding_transcript_exon_variant	Exon 7 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GMDS-DT	ENST00000505870.5	n.7980G>A		non_coding_transcript_exon_variant	Exon 3 of 3	1
GMDS-DT	ENST00000529893.6	n.1728G>A		non_coding_transcript_exon_variant	Exon 7 of 7	5
GMDS-DT	ENST00000531092.7	n.1797G>A		non_coding_transcript_exon_variant	Exon 8 of 8	3

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20635 AN: 151366 Hom.: 1544 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.0879

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.0647

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.132

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.136 AC: 20651 AN: 151482 Hom.: 1544 Cov.: 32 AF XY: 0.138 AC XY: 10214 AN XY: 73986

African (AFR) AF: 0.114 AC: 4695 AN: 41296

American (AMR) AF: 0.171 AC: 2589 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.0647 AC: 224 AN: 3464

East Asian (EAS) AF: 0.170 AC: 876 AN: 5138

South Asian (SAS) AF: 0.207 AC: 997 AN: 4808

European-Finnish (FIN) AF: 0.139 AC: 1448 AN: 10396

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9438 AN: 67888

Other (OTH) AF: 0.133 AC: 281 AN: 2108

Alfa AF: 0.138 Hom.: 2176

Bravo AF: 0.135

Asia WGS AF: 0.196 AC: 684 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	22
DANN	Benign	0.74
PhyloP100		4.1

Splicing

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

Other links and lift over

dbSNP: rs3734505; hg19: chr6-2413588;