10-27340817-G-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

ENSG00000215409 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000262412	ENST00000787620.1	n.302-13889G>C		intron_variant	Intron 2 of 3
ENSG00000262412	ENST00000787621.1	n.546-16270G>C		intron_variant	Intron 3 of 3

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

African (AFR) AF: 0.928 AC: 5008 AN: 5394

American (AMR) AF: 0.775 AC: 10470 AN: 13516

Ashkenazi Jewish (ASJ) AF: 0.765 AC: 4818 AN: 6302

East Asian (EAS) AF: 0.677 AC: 8796 AN: 12988

South Asian (SAS) AF: 0.648 AC: 13434 AN: 20740

European-Finnish (FIN) AF: 0.705 AC: 18793 AN: 26650

Middle Eastern (MID) AF: 0.753 AC: 1857 AN: 2466

European-Non Finnish (NFE) AF: 0.722 AC: 92422 AN: 127994

Other (OTH) AF: 0.742 AC: 8378 AN: 11296

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

African (AFR) AF: 0.898 AC: 35650 AN: 39718

American (AMR) AF: 0.722 AC: 10990 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.716 AC: 2482 AN: 3468

East Asian (EAS) AF: 0.567 AC: 2935 AN: 5172

South Asian (SAS) AF: 0.642 AC: 3092 AN: 4814

European-Finnish (FIN) AF: 0.695 AC: 7317 AN: 10534

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.668 AC: 45401 AN: 67928

Other (OTH) AF: 0.713 AC: 1492 AN: 2094

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
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; COSMIC: COSV69921087;