chr17-36772138-T-G

Variant names:

• chr17-36772138-T-G
• rs295885
• ENST00000847897.1:n.1199T>G

Variant summary

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

The ENST00000847897.1(ENSG00000275613):​n.1199T>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 0.234 in 152,206 control chromosomes in the GnomAD database, including 4,696 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 0.23 (4696 hom., cov: 33)
• Consequence: ENSG00000275613 ENST00000847897.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809
• Publications: 1 publications found

Genes affected

ENSG00000275613 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (Cadd=1.162).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000847897.1. 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
	ENSG00000275613	ENST00000847897.1		n.1199T>G		non_coding_transcript_exon	Exon 5 of 5
	ENSG00000275613	ENST00000847898.1		n.807T>G		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000275613	ENST00000847899.1		n.1331T>G		non_coding_transcript_exon	Exon 6 of 6

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35562 AN: 152088 Hom.: 4684 Cov.: 33

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.234 AC: 35581 AN: 152206 Hom.: 4696 Cov.: 33 AF XY: 0.235 AC XY: 17500 AN XY: 74404

African (AFR) AF: 0.112 AC: 4669 AN: 41550

American (AMR) AF: 0.297 AC: 4544 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 951 AN: 3470

East Asian (EAS) AF: 0.338 AC: 1754 AN: 5182

South Asian (SAS) AF: 0.284 AC: 1373 AN: 4830

European-Finnish (FIN) AF: 0.270 AC: 2853 AN: 10586

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18442 AN: 67988

Other (OTH) AF: 0.263 AC: 555 AN: 2110

Alfa AF: 0.140 Hom.: 294

Bravo AF: 0.234

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
CADD	Benign	1.2
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs295885;