chr4-10285644-A-G

Variant names:

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

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100422637		n.10285644A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000250505	ENST00000506077.1	n.65T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

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 v4.3

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

Other links and lift over

dbSNP: rs10489068; hg19: chr4-10287268;