rs3825944

Variant names:

• chr15-74375417-G-A
• rs3825944
• ENST00000611178.1:n.740G>A

Variant summary

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

The ENST00000611178.1(ENSG00000274937):​n.740G>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 0.255 in 152,084 control chromosomes in the GnomAD database, including 6,066 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 (6066 hom., cov: 32)
  • Exomes 𝑓: 0.10 (0 hom.)
• Consequence: ENSG00000274937 ENST00000611178.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.353

Genes affected

ENSG00000274937 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.426 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
ENSG00000274937	ENST00000611178.1	n.740G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38662 AN: 151956 Hom.: 6041 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: 0.435

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.227

GnomAD4 exome AF: 0.100 AC: 1 AN: 10 Hom.: 0 Cov.: 0 AF XY: 0.125 AC XY: 1 AN XY: 8

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.255 AC: 38753 AN: 152074 Hom.: 6066 Cov.: 32 AF XY: 0.257 AC XY: 19108 AN XY: 74358

Gnomad4 AFR AF: 0.431

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.435

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.170

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.233

Alfa AF: 0.199 Hom.: 844

Bravo AF: 0.264

Asia WGS AF: 0.434 AC: 1512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	10
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3825944; hg19: chr15-74667758;