rs4887139

Variant names:

• chr15-74369604-G-A
• rs4887139
• ENST00000568496.3:n.3410G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000568496.3(ENSG00000261821):​n.3410G>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: ENSG00000261821 ENST00000568496.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.646
• Publications: 7 publications found

Genes affected

ENSG00000261821 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000568496.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000261821	ENST00000568496.3	TSL:2	n.3410G>A		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000261821	ENST00000783990.1		n.478-877G>A		intron	N/A
	ENSG00000261821	ENST00000783991.1		n.553-877G>A		intron	N/A

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

African (AFR) AF: 1.00 AC: 6 AN: 6

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.500 AC: 2 AN: 4

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.867 AC: 26 AN: 30

Other (OTH) AF: 0.875 AC: 7 AN: 8

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

African (AFR) AF: 0.966 AC: 40108 AN: 41508

American (AMR) AF: 0.843 AC: 12885 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.838 AC: 2909 AN: 3470

East Asian (EAS) AF: 0.869 AC: 4499 AN: 5176

South Asian (SAS) AF: 0.873 AC: 4208 AN: 4820

European-Finnish (FIN) AF: 0.885 AC: 9382 AN: 10602

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.849 AC: 57716 AN: 68000

Other (OTH) AF: 0.842 AC: 1776 AN: 2110

Alfa AF: 0.867 Hom.: 12984

Bravo AF: 0.884

Asia WGS AF: 0.876 AC: 3046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.9
DANN	Benign	0.47
PhyloP100		0.65

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4887139;

hg19: chr15-74661945;