10-27340817-G-T

Variant names:

• chr10-27340817-G-T
• rs237596
• ENST00000422707.1:n.274C>A

Variant summary

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

The ENST00000422707.1(ENSG00000215409):​n.274C>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 0.00000666 in 150,200 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: 𝑓 0.0000067 (0 hom., cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000215409 ENST00000422707.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.904
• Publications: 2 publications found

Genes affected

ENSG00000215409 (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=-0.75).

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
ENSG00000215409	ENST00000422707.1	n.274C>A		non_coding_transcript_exon_variant	Exon 2 of 6	6
ENSG00000262412	ENST00000787620.1	n.302-13889G>T		intron_variant	Intron 2 of 3
ENSG00000262412	ENST00000787621.1	n.546-16270G>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.00000666 AC: 1 AN: 150086 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 227796 Hom.: 0 Cov.: 3 AF XY: 0.00 AC XY: 0 AN XY: 129252

African (AFR) AF: 0.00 AC: 0 AN: 5398

American (AMR) AF: 0.00 AC: 0 AN: 13530

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 6308

East Asian (EAS) AF: 0.00 AC: 0 AN: 13000

South Asian (SAS) AF: 0.00 AC: 0 AN: 20802

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 26692

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2468

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 128284

Other (OTH) AF: 0.00 AC: 0 AN: 11314

GnomAD4 genome AF: 0.00000666 AC: 1 AN: 150200 Hom.: 0 Cov.: 31 AF XY: 0.0000136 AC XY: 1 AN XY: 73388

African (AFR) AF: 0.00 AC: 0 AN: 39732

American (AMR) AF: 0.00 AC: 0 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5174

South Asian (SAS) AF: 0.000208 AC: 1 AN: 4816

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10550

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67934

Other (OTH) AF: 0.00 AC: 0 AN: 2098

Alfa AF: 0.00 Hom.: 4555

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	1.9
DANN	Benign	0.31
PhyloP100		0.90

Splicing

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

Other links and lift over

dbSNP: rs237596; hg19: chr10-27629746;