10-27340817-G-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000422707.1(ENSG00000215409):​n.274C>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 0.726 in 377,496 control chromosomes in the GnomAD database, including 101,356 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 0.73 (41588 hom., cov: 31)
  • Exomes 𝑓: 0.72 (59768 hom.)
• Consequence: ENSG00000215409 ENST00000422707.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.904

Genes affected

ENSG00000215409 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.89 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
ENSG00000215409	ENST00000422707.1	n.274C>G		non_coding_transcript_exon_variant	Exon 2 of 6	6

Frequencies

GnomAD3 genomes AF: 0.733 AC: 110030 AN: 150036 Hom.: 41530 Cov.: 31

Gnomad AFR AF: 0.897

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.722

Gnomad ASJ AF: 0.716

Gnomad EAS AF: 0.569

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.716

GnomAD4 exome AF: 0.721 AC: 163976 AN: 227346 Hom.: 59768 Cov.: 3 AF XY: 0.713 AC XY: 91976 AN XY: 128984

Gnomad4 AFR exome AF: 0.928

Gnomad4 AMR exome AF: 0.775

Gnomad4 ASJ exome AF: 0.765

Gnomad4 EAS exome AF: 0.677

Gnomad4 SAS exome AF: 0.648

Gnomad4 FIN exome AF: 0.705

Gnomad4 NFE exome AF: 0.722

Gnomad4 OTH exome AF: 0.742

GnomAD4 genome AF: 0.734 AC: 110148 AN: 150150 Hom.: 41588 Cov.: 31 AF XY: 0.733 AC XY: 53762 AN XY: 73362

Gnomad4 AFR AF: 0.898

Gnomad4 AMR AF: 0.722

Gnomad4 ASJ AF: 0.716

Gnomad4 EAS AF: 0.567

Gnomad4 SAS AF: 0.642

Gnomad4 FIN AF: 0.695

Gnomad4 NFE AF: 0.668

Gnomad4 OTH AF: 0.713

Alfa AF: 0.705 Hom.: 4555

Bravo AF: 0.745

Asia WGS AF: 0.631 AC: 2193 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.8
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs237596; hg19: chr10-27629746; COSMIC: COSV69921087;