rs3138034

Variant names:

• chr17-34315706-C-T
• rs3138034
• ENST00000849825.1:n.147+3218G>A

Variant summary

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

The ENST00000849825.1(ENSG00000310445):​n.147+3218G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,004 control chromosomes in the GnomAD database, including 2,149 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 0.15 (2149 hom., cov: 31)
• Consequence: ENSG00000310445 ENST00000849825.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07
• Publications: 8 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 = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310445	ENST00000849825.1	n.147+3218G>A		intron_variant	Intron 1 of 1
ENSG00000310445	ENST00000849826.1	n.34+3218G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22388 AN: 151886 Hom.: 2149 Cov.: 31

Gnomad AFR AF: 0.0374

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.0856

Gnomad SAS AF: 0.0906

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.147 AC: 22386 AN: 152004 Hom.: 2149 Cov.: 31 AF XY: 0.145 AC XY: 10742 AN XY: 74294

African (AFR) AF: 0.0373 AC: 1546 AN: 41496

American (AMR) AF: 0.113 AC: 1725 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 666 AN: 3466

East Asian (EAS) AF: 0.0856 AC: 441 AN: 5154

South Asian (SAS) AF: 0.0908 AC: 438 AN: 4822

European-Finnish (FIN) AF: 0.208 AC: 2197 AN: 10560

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14855 AN: 67928

Other (OTH) AF: 0.134 AC: 284 AN: 2114

Alfa AF: 0.186 Hom.: 410

Bravo AF: 0.135

Asia WGS AF: 0.0770 AC: 271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.0
DANN	Benign	0.20
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs3138034; hg19: chr17-32642725;