rs727345

Variant names:

• chr10-31610145-A-G
• rs727345
• ENST00000662998.1:n.320T>C

Variant summary

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

The ENST00000662998.1(ENSG00000286694):​n.320T>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 0.482 in 152,022 control chromosomes in the GnomAD database, including 21,011 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 0.48 (21011 hom., cov: 32)
• Consequence: ENSG00000286694 ENST00000662998.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.563
• Publications: 7 publications found

Genes affected

ENSG00000286694 (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 (NFE) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376484	XR_930803.3	n.431T>C		non_coding_transcript_exon_variant	Exon 3 of 3
LOC105376484	XR_930804.3	n.366T>C		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286694	ENST00000662998.1	n.320T>C		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000286694	ENST00000795997.1	n.473T>C		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73218 AN: 151904 Hom.: 20998 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.482 AC: 73236 AN: 152022 Hom.: 21011 Cov.: 32 AF XY: 0.477 AC XY: 35450 AN XY: 74318

African (AFR) AF: 0.161 AC: 6666 AN: 41494

American (AMR) AF: 0.584 AC: 8924 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1807 AN: 3472

East Asian (EAS) AF: 0.379 AC: 1952 AN: 5146

South Asian (SAS) AF: 0.442 AC: 2129 AN: 4814

European-Finnish (FIN) AF: 0.544 AC: 5736 AN: 10550

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.652 AC: 44332 AN: 67948

Other (OTH) AF: 0.486 AC: 1024 AN: 2106

Alfa AF: 0.601 Hom.: 47315

Bravo AF: 0.475

Asia WGS AF: 0.368 AC: 1282 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	2.6
DANN	Benign	0.49
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs727345; hg19: chr10-31899073;