rs10981985

Variant names:

• chr9-97405289-G-A
• rs10981985
• ENST00000667253.2:n.65-499C>T

Variant summary

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

The ENST00000667253.2(ENSG00000286375):​n.65-499C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,166 control chromosomes in the GnomAD database, including 1,536 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 0.13 (1536 hom., cov: 32)
• Consequence: ENSG00000286375 ENST00000667253.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190
• Publications: 2 publications found

Genes affected

ENSG00000286375 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286375	ENST00000667253.2	n.65-499C>T		intron_variant	Intron 1 of 1
ENSG00000286375	ENST00000778879.1	n.58-3739C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.125 AC: 19006 AN: 152050 Hom.: 1527 Cov.: 32

Gnomad AFR AF: 0.0552

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.0643

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.125 AC: 19025 AN: 152166 Hom.: 1536 Cov.: 32 AF XY: 0.130 AC XY: 9700 AN XY: 74390

African (AFR) AF: 0.0552 AC: 2292 AN: 41530

American (AMR) AF: 0.235 AC: 3594 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0643 AC: 223 AN: 3468

East Asian (EAS) AF: 0.284 AC: 1471 AN: 5172

South Asian (SAS) AF: 0.163 AC: 787 AN: 4824

European-Finnish (FIN) AF: 0.159 AC: 1687 AN: 10582

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8609 AN: 68002

Other (OTH) AF: 0.130 AC: 274 AN: 2102

Alfa AF: 0.127 Hom.: 601

Bravo AF: 0.129

Asia WGS AF: 0.224 AC: 777 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.6
DANN	Benign	0.43
PhyloP100		-0.019

Splicing

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

Other links and lift over

dbSNP: rs10981985; hg19: chr9-100167571;