rs3825944

Positions:

• chr15-74375417-G-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: ENST00000611178.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.353

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000611178.1	n.740G>A		non_coding_transcript_exon_variant	1/1

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;