rs10969139

Variant names:

• chr9-29412340-T-C
• rs10969139
• ENST00000775037.1:n.254+38049A>G

Variant summary

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

The ENST00000775037.1(ENSG00000300910):​n.254+38049A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0351 in 151,000 control chromosomes in the GnomAD database, including 123 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 (123 hom., cov: 32)
• Consequence: ENSG00000300910 ENST00000775037.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.97
• 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 = 0.0821 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+38049A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0351 AC: 5297 AN: 150882 Hom.: 123 Cov.: 32

Gnomad AFR AF: 0.0350

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.0303

Gnomad ASJ AF: 0.0250

Gnomad EAS AF: 0.0890

Gnomad SAS AF: 0.0263

Gnomad FIN AF: 0.0219

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0340

Gnomad OTH AF: 0.0300

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

GnomAD4 genome AF: 0.0351 AC: 5301 AN: 151000 Hom.: 123 Cov.: 32 AF XY: 0.0343 AC XY: 2533 AN XY: 73758

African (AFR) AF: 0.0350 AC: 1447 AN: 41374

American (AMR) AF: 0.0304 AC: 459 AN: 15100

Ashkenazi Jewish (ASJ) AF: 0.0250 AC: 86 AN: 3438

East Asian (EAS) AF: 0.0888 AC: 456 AN: 5134

South Asian (SAS) AF: 0.0268 AC: 129 AN: 4822

European-Finnish (FIN) AF: 0.0219 AC: 232 AN: 10608

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

European-Non Finnish (NFE) AF: 0.0340 AC: 2287 AN: 67232

Other (OTH) AF: 0.0297 AC: 62 AN: 2090

Alfa AF: 0.0342 Hom.: 23

Bravo AF: 0.0381

Asia WGS AF: 0.0440 AC: 153 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	0.015
DANN	Benign	0.46
PhyloP100		-3.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10969139;

hg19: chr9-29412338;

COSMIC: COSV69456967;