rs4887139

Positions:

• chr15-74369604-G-A
• chr15-74369604-G-C
• chr15-74369604-G-T

Variant summary

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

The ENST00000568496.2(ENSG00000261821):​n.3339G>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 0.883 in 152,222 control chromosomes in the GnomAD database, including 59,621 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 0.88 (59604 hom., cov: 31)
  • Exomes 𝑓: 0.84 (17 hom.)
• Consequence: ENST00000568496.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.646

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.958 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124903524	XR_007064709.1	n.3987G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000568496.2	n.3339G>A		non_coding_transcript_exon_variant	3/3	2

Frequencies

GnomAD3 genomes AF: 0.883 AC: 134246 AN: 152054 Hom.: 59533 Cov.: 31

Gnomad AFR AF: 0.966

Gnomad AMI AF: 0.722

Gnomad AMR AF: 0.843

Gnomad ASJ AF: 0.838

Gnomad EAS AF: 0.868

Gnomad SAS AF: 0.873

Gnomad FIN AF: 0.885

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.849

Gnomad OTH AF: 0.841

GnomAD4 exome AF: 0.840 AC: 42 AN: 50 Hom.: 17 Cov.: 0 AF XY: 0.833 AC XY: 35 AN XY: 42

Gnomad4 AFR exome AF: 1.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.867

Gnomad4 OTH exome AF: 0.875

GnomAD4 genome AF: 0.883 AC: 134377 AN: 152172 Hom.: 59604 Cov.: 31 AF XY: 0.881 AC XY: 65526 AN XY: 74378

Gnomad4 AFR AF: 0.966

Gnomad4 AMR AF: 0.843

Gnomad4 ASJ AF: 0.838

Gnomad4 EAS AF: 0.869

Gnomad4 SAS AF: 0.873

Gnomad4 FIN AF: 0.885

Gnomad4 NFE AF: 0.849

Gnomad4 OTH AF: 0.842

Alfa AF: 0.851 Hom.: 3110

Bravo AF: 0.884

Asia WGS AF: 0.876 AC: 3046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.9
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4887139; hg19: chr15-74661945;