rs10489068

Variant names:

• chr4-10285644-A-G
• rs10489068
• ENST00000506077.1:n.65T>C

Your query was ambiguous. Multiple possible variants found:

• chr4-10285644-A-G
• chr4-10285644-A-T

Variant summary

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

The ENST00000506077.1(ENSG00000250505):​n.65T>C 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 0.631 in 152,112 control chromosomes in the GnomAD database, including 30,654 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 0.63 (30629 hom., cov: 32)
  • Exomes 𝑓: 0.72 (25 hom.)
• Consequence: ENSG00000250505 ENST00000506077.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900
• Publications: 7 publications found

Genes affected

ENSG00000250505 (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 (NFE) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000506077.1. 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
	ENSG00000250505	ENST00000506077.1	TSL:6	n.65T>C		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.631 AC: 95793 AN: 151890 Hom.: 30609 Cov.: 32

Gnomad AFR AF: 0.538

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.623

GnomAD4 exome AF: 0.721 AC: 75 AN: 104 Hom.: 25 Cov.: 0 AF XY: 0.729 AC XY: 51 AN XY: 70

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.625 AC: 5 AN: 8

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 0.721 AC: 62 AN: 86

Other (OTH) AF: 0.833 AC: 5 AN: 6

GnomAD4 genome AF: 0.631 AC: 95862 AN: 152008 Hom.: 30629 Cov.: 32 AF XY: 0.632 AC XY: 46962 AN XY: 74308

African (AFR) AF: 0.538 AC: 22305 AN: 41450

American (AMR) AF: 0.619 AC: 9442 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.586 AC: 2034 AN: 3470

East Asian (EAS) AF: 0.540 AC: 2784 AN: 5154

South Asian (SAS) AF: 0.683 AC: 3291 AN: 4818

European-Finnish (FIN) AF: 0.693 AC: 7336 AN: 10588

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.687 AC: 46672 AN: 67958

Other (OTH) AF: 0.618 AC: 1306 AN: 2112

Alfa AF: 0.606 Hom.: 3336

Bravo AF: 0.616

Asia WGS AF: 0.634 AC: 2204 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.58
PhyloP100		-0.090

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: rs10489068;

hg19: chr4-10287268;