15-74374851-G-A

Variant names:

• chr15-74374851-G-A
• rs12438594
• ENST00000611178.1:n.174G>A

Variant summary

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

The ENST00000611178.1(ENSG00000274937):​n.174G>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 0.254 in 152,474 control chromosomes in the GnomAD database, including 6,058 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 0.25 (6046 hom., cov: 32)
  • Exomes 𝑓: 0.17 (12 hom.)
• Consequence: ENSG00000274937 ENST00000611178.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.307
• Publications: 2 publications found

Genes affected

ENSG00000274937 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000611178.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000274937	ENST00000611178.1	TSL:6	n.174G>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000302041	ENST00000783573.1		n.116-4773C>T		intron	N/A
	ENSG00000302041	ENST00000783574.1		n.186+495C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38596 AN: 151776 Hom.: 6021 Cov.: 32

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.227

GnomAD4 exome AF: 0.172 AC: 100 AN: 580 Hom.: 12 Cov.: 0 AF XY: 0.193 AC XY: 80 AN XY: 414

African (AFR) AF: 0.571 AC: 8 AN: 14

American (AMR) AF: 0.250 AC: 3 AN: 12

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 2 AN: 6

East Asian (EAS) AF: 0.429 AC: 6 AN: 14

South Asian (SAS) AF: 0.625 AC: 5 AN: 8

European-Finnish (FIN) AF: 0.188 AC: 12 AN: 64

Middle Eastern (MID) AF: 0.500 AC: 3 AN: 6

European-Non Finnish (NFE) AF: 0.127 AC: 53 AN: 416

Other (OTH) AF: 0.200 AC: 8 AN: 40

GnomAD4 genome AF: 0.255 AC: 38687 AN: 151894 Hom.: 6046 Cov.: 32 AF XY: 0.257 AC XY: 19049 AN XY: 74208

African (AFR) AF: 0.431 AC: 17824 AN: 41374

American (AMR) AF: 0.211 AC: 3222 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 662 AN: 3470

East Asian (EAS) AF: 0.433 AC: 2234 AN: 5158

South Asian (SAS) AF: 0.383 AC: 1833 AN: 4786

European-Finnish (FIN) AF: 0.170 AC: 1801 AN: 10578

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10377 AN: 67940

Other (OTH) AF: 0.233 AC: 491 AN: 2110

Alfa AF: 0.220 Hom.: 1635

Bravo AF: 0.264

Asia WGS AF: 0.434 AC: 1511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.6
DANN	Benign	0.61
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs12438594; hg19: chr15-74667192;