rs3138035

Variant names:

• chr17-34318930-C-T
• rs3138035
• ENST00000849825.1:n.141G>A

Variant summary

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

The ENST00000849825.1(ENSG00000310445):​n.141G>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 0.274 in 152,358 control chromosomes in the GnomAD database, including 6,739 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 0.27 (6726 hom., cov: 33)
  • Exomes 𝑓: 0.38 (13 hom.)
• Consequence: ENSG00000310445 ENST00000849825.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92
• Publications: 17 publications found

Genes affected

ENSG00000310445 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000849825.1. 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
	ENSG00000310445	ENST00000849825.1		n.141G>A		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000310445	ENST00000849826.1		n.28G>A		non_coding_transcript_exon	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41600 AN: 152022 Hom.: 6726 Cov.: 33

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.0953

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.274

GnomAD4 exome AF: 0.375 AC: 81 AN: 216 Hom.: 13 AF XY: 0.331 AC XY: 39 AN XY: 118

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.355 AC: 49 AN: 138

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.405 AC: 30 AN: 74

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.273 AC: 41596 AN: 152142 Hom.: 6726 Cov.: 33 AF XY: 0.274 AC XY: 20383 AN XY: 74358

African (AFR) AF: 0.121 AC: 5005 AN: 41534

American (AMR) AF: 0.218 AC: 3341 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1261 AN: 3470

East Asian (EAS) AF: 0.0954 AC: 494 AN: 5180

South Asian (SAS) AF: 0.242 AC: 1169 AN: 4824

European-Finnish (FIN) AF: 0.414 AC: 4373 AN: 10556

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.368 AC: 25020 AN: 67968

Other (OTH) AF: 0.270 AC: 570 AN: 2112

Alfa AF: 0.326 Hom.: 16580

Bravo AF: 0.249

Asia WGS AF: 0.151 AC: 529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.057
DANN	Benign	0.45
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs3138035; hg19: chr17-32645949;