rs2036657

Variant names:

• chr17-4721864-G-A
• rs2036657
• ENST00000786507.1:n.465C>T

Your query was ambiguous. Multiple possible variants found:

• chr17-4721864-G-A
• chr17-4721864-G-C

Variant summary

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

The ENST00000786507.1(ENSG00000302420):​n.465C>T 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 0.63 in 152,104 control chromosomes in the GnomAD database, including 31,362 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 0.63 (31362 hom., cov: 32)
• Consequence: ENSG00000302420 ENST00000786507.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22
• Publications: 26 publications found

Genes affected

ENSG00000302420 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.801 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
ENSG00000302420	ENST00000786507.1	n.465C>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000302420	ENST00000786504.1	n.38-4135C>T		intron_variant	Intron 1 of 1
ENSG00000302420	ENST00000786505.1	n.131+296C>T		intron_variant	Intron 2 of 3
ENSG00000302420	ENST00000786506.1	n.48-2697C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.630 AC: 95697 AN: 151986 Hom.: 31334 Cov.: 32

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.822

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.769

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.686

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.630 AC: 95758 AN: 152104 Hom.: 31362 Cov.: 32 AF XY: 0.638 AC XY: 47414 AN XY: 74362

African (AFR) AF: 0.435 AC: 18024 AN: 41476

American (AMR) AF: 0.689 AC: 10530 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.678 AC: 2353 AN: 3470

East Asian (EAS) AF: 0.822 AC: 4254 AN: 5176

South Asian (SAS) AF: 0.809 AC: 3898 AN: 4816

European-Finnish (FIN) AF: 0.769 AC: 8139 AN: 10590

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.686 AC: 46633 AN: 67982

Other (OTH) AF: 0.619 AC: 1308 AN: 2112

Alfa AF: 0.660 Hom.: 50283

Bravo AF: 0.613

Asia WGS AF: 0.794 AC: 2762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	6.0
DANN	Benign	0.83
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs2036657; hg19: chr17-4625159;