chr9-29423653-A-G

Variant names:

• chr9-29423653-A-G
• rs10813083
• ENST00000775037.1:n.254+26736T>C

Variant summary

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

The ENST00000775037.1(ENSG00000300910):​n.254+26736T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0428 in 151,518 control chromosomes in the GnomAD database, including 187 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 0.043 (187 hom., cov: 32)
• Consequence: ENSG00000300910 ENST00000775037.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.43
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0829 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300910	ENST00000775037.1		n.254+26736T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0427 AC: 6466 AN: 151400 Hom.: 183 Cov.: 32

Gnomad AFR AF: 0.0609

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.0330

Gnomad ASJ AF: 0.0252

Gnomad EAS AF: 0.0898

Gnomad SAS AF: 0.0265

Gnomad FIN AF: 0.0222

Gnomad MID AF: 0.0414

Gnomad NFE AF: 0.0342

Gnomad OTH AF: 0.0380

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

GnomAD4 genome AF: 0.0428 AC: 6487 AN: 151518 Hom.: 187 Cov.: 32 AF XY: 0.0421 AC XY: 3118 AN XY: 74040

African (AFR) AF: 0.0613 AC: 2540 AN: 41456

American (AMR) AF: 0.0331 AC: 502 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.0252 AC: 87 AN: 3458

East Asian (EAS) AF: 0.0896 AC: 459 AN: 5120

South Asian (SAS) AF: 0.0269 AC: 130 AN: 4824

European-Finnish (FIN) AF: 0.0222 AC: 235 AN: 10608

Middle Eastern (MID) AF: 0.0411 AC: 12 AN: 292

European-Non Finnish (NFE) AF: 0.0342 AC: 2310 AN: 67578

Other (OTH) AF: 0.0376 AC: 79 AN: 2102

Alfa AF: 0.0383 Hom.: 17

Bravo AF: 0.0465

Asia WGS AF: 0.0520 AC: 179 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.021
DANN	Benign	0.76
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs10813083; hg19: chr9-29423651; COSMIC: COSV69456987;