ENST00000660544.1:n.866T>C

Variant names:

• chr10-4033464-T-C
• rs1886946
• ENST00000660544.1:n.866T>C

Variant summary

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

The ENST00000660544.1(ENSG00000227101):​n.866T>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 0.458 in 151,872 control chromosomes in the GnomAD database, including 18,131 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 0.46 (18131 hom., cov: 31)
• Consequence: ENSG00000227101 ENST00000660544.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207
• Publications: 1 publications found

Genes affected

ENSG00000227101 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.708 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984195	NR_176060.1	n.613+1761T>C		intron_variant	Intron 2 of 9
LOC107984195	NR_176062.1	n.613+1761T>C		intron_variant	Intron 2 of 3
LOC107984195	NR_176063.1	n.867+1761T>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000227101	ENST00000660544.1	n.866T>C		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000227101	ENST00000656775.1	n.689+1761T>C		intron_variant	Intron 2 of 2
ENSG00000227101	ENST00000658139.1	n.568+1761T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.458 AC: 69480 AN: 151754 Hom.: 18091 Cov.: 31

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.476

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.458 AC: 69578 AN: 151872 Hom.: 18131 Cov.: 31 AF XY: 0.446 AC XY: 33131 AN XY: 74224

African (AFR) AF: 0.715 AC: 29580 AN: 41398

American (AMR) AF: 0.356 AC: 5428 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.521 AC: 1810 AN: 3472

East Asian (EAS) AF: 0.329 AC: 1690 AN: 5130

South Asian (SAS) AF: 0.300 AC: 1449 AN: 4826

European-Finnish (FIN) AF: 0.260 AC: 2737 AN: 10536

Middle Eastern (MID) AF: 0.534 AC: 156 AN: 292

European-Non Finnish (NFE) AF: 0.373 AC: 25315 AN: 67942

Other (OTH) AF: 0.478 AC: 1005 AN: 2104

Alfa AF: 0.412 Hom.: 36910

Bravo AF: 0.480

Asia WGS AF: 0.365 AC: 1268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.42
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs1886946; hg19: chr10-4075656;