rs17585937

Variant names:

• chr4-40044067-C-A
• rs17585937
• ENST00000381811.2:n.463G>T

Your query was ambiguous. Multiple possible variants found:

• chr4-40044067-C-A
• chr4-40044067-C-G
• chr4-40044067-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000381811.2(ENSG00000293349):​n.463G>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 0.00000374 in 534,342 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000037 (0 hom.)
• Consequence: ENSG00000293349 ENST00000381811.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.564
• Publications: 0 publications found

Genes affected

ENSG00000293349 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC344967	NR_027277.2	n.463G>T		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293349	ENST00000381811.2	n.463G>T		non_coding_transcript_exon_variant	Exon 3 of 3	2
ENSG00000205794	ENST00000507914.2	n.69G>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000374 AC: 2 AN: 534342 Hom.: 0 Cov.: 4 AF XY: 0.00000347 AC XY: 1 AN XY: 288360

African (AFR) AF: 0.00 AC: 0 AN: 15422

American (AMR) AF: 0.00 AC: 0 AN: 33694

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18830

East Asian (EAS) AF: 0.00 AC: 0 AN: 31158

South Asian (SAS) AF: 0.0000162 AC: 1 AN: 61882

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 36984

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3850

European-Non Finnish (NFE) AF: 0.00000329 AC: 1 AN: 303630

Other (OTH) AF: 0.00 AC: 0 AN: 28892

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.7
DANN	Benign	0.68
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs17585937; hg19: chr4-40045687;