rs10981985

chr9-97405289-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000667253.1(ENSG00000286375):n.52-499C>T variant causes a intron, non coding transcript 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: ENST00000667253.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000667253.1	n.52-499C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0552

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.0643

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.130

Alfa AF: 0.115 Hom.: 273

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10981985; hg19: chr9-100167571;