rs10969138

Variant names:

• chr9-29409916-G-A
• rs10969138
• ENST00000775037.1:n.254+40473C>T

Variant summary

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

The ENST00000775037.1(ENSG00000300910):​n.254+40473C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0352 in 150,988 control chromosomes in the GnomAD database, including 122 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 0.035 (122 hom., cov: 32)
• Consequence: ENSG00000300910 ENST00000775037.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.603
• Publications: 0 publications found

Genes affected

ENSG00000300910 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0822 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000775037.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300910	ENST00000775037.1		n.254+40473C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0352 AC: 5304 AN: 150870 Hom.: 122 Cov.: 32

Gnomad AFR AF: 0.0346

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.0305

Gnomad ASJ AF: 0.0253

Gnomad EAS AF: 0.0891

Gnomad SAS AF: 0.0269

Gnomad FIN AF: 0.0224

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0342

Gnomad OTH AF: 0.0300

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

GnomAD4 genome AF: 0.0352 AC: 5308 AN: 150988 Hom.: 122 Cov.: 32 AF XY: 0.0344 AC XY: 2536 AN XY: 73764

African (AFR) AF: 0.0346 AC: 1429 AN: 41302

American (AMR) AF: 0.0306 AC: 462 AN: 15094

Ashkenazi Jewish (ASJ) AF: 0.0253 AC: 87 AN: 3442

East Asian (EAS) AF: 0.0889 AC: 455 AN: 5116

South Asian (SAS) AF: 0.0274 AC: 132 AN: 4820

European-Finnish (FIN) AF: 0.0224 AC: 236 AN: 10556

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0341 AC: 2300 AN: 67360

Other (OTH) AF: 0.0296 AC: 62 AN: 2092

Alfa AF: 0.0351 Hom.: 145

Bravo AF: 0.0380

Asia WGS AF: 0.0440 AC: 155 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.12
DANN	Benign	0.32
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs10969138; hg19: chr9-29409914; COSMIC: COSV69456965;