rs3734505

chr6-2413354-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_046229.1(GMDS-DT):n.1351G>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 NR_046229.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.06

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
GMDS-DT	NR_046229.1	n.1351G>A		non_coding_transcript_exon_variant	7/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GMDS-DT	ENST00000659523.1	n.286-67480G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 ASJ exome AF: 0.00

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

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.0647

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.133

Alfa AF: 0.138 Hom.: 1456

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3734505; hg19: chr6-2413588;