15-74370470-A-G

Position:

• chr15-74370470-A-G

Variant summary

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

The ENST00000568496.2(ENSG00000261821):​n.4205A>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 0.316 in 152,128 control chromosomes in the GnomAD database, including 9,638 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 0.32 (9635 hom., cov: 32)
  • Exomes 𝑓: 0.36 (3 hom.)
• Consequence: ENSG00000261821 ENST00000568496.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.529

Genes affected

ENSG00000261821 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124903524	XR_007064709.1	n.4853A>G		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000261821	ENST00000568496.2	n.4205A>G		non_coding_transcript_exon_variant	3/3	2

Frequencies

GnomAD3 genomes AF: 0.316 AC: 48036 AN: 151988 Hom.: 9596 Cov.: 32

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.292

GnomAD4 exome AF: 0.364 AC: 8 AN: 22 Hom.: 3 Cov.: 0 AF XY: 0.429 AC XY: 6 AN XY: 14

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.250

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.316 AC: 48139 AN: 152106 Hom.: 9635 Cov.: 32 AF XY: 0.319 AC XY: 23694 AN XY: 74366

Gnomad4 AFR AF: 0.560

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.459

Gnomad4 SAS AF: 0.436

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.297

Alfa AF: 0.215 Hom.: 5384

Bravo AF: 0.331

Asia WGS AF: 0.474 AC: 1649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.87
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16968478; hg19: chr15-74662811;