chr9-35155911-A-G

Variant names:

• chr9-35155911-A-G
• rs10081672
• ENST00000836210.1:n.422+185T>C

Variant summary

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

The ENST00000836210.1(ENSG00000308740):​n.422+185T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 152,010 control chromosomes in the GnomAD database, including 11,503 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 0.38 (11503 hom., cov: 31)
• Consequence: ENSG00000308740 ENST00000836210.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.889
• Publications: 8 publications found

Genes affected

ENSG00000308740 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000836210.1. 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
	ENSG00000308740	ENST00000836210.1		n.422+185T>C		intron	N/A
	ENSG00000308740	ENST00000836211.1		n.722+185T>C		intron	N/A
	ENSG00000308740	ENST00000836212.1		n.962+185T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57615 AN: 151892 Hom.: 11486 Cov.: 31

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.0133

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.379 AC: 57677 AN: 152010 Hom.: 11503 Cov.: 31 AF XY: 0.374 AC XY: 27790 AN XY: 74316

African (AFR) AF: 0.365 AC: 15139 AN: 41440

American (AMR) AF: 0.433 AC: 6613 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1226 AN: 3468

East Asian (EAS) AF: 0.0135 AC: 70 AN: 5184

South Asian (SAS) AF: 0.181 AC: 874 AN: 4818

European-Finnish (FIN) AF: 0.466 AC: 4919 AN: 10566

Middle Eastern (MID) AF: 0.370 AC: 108 AN: 292

European-Non Finnish (NFE) AF: 0.406 AC: 27580 AN: 67938

Other (OTH) AF: 0.383 AC: 809 AN: 2112

Alfa AF: 0.368 Hom.: 3569

Bravo AF: 0.376

Asia WGS AF: 0.136 AC: 477 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.24
PhyloP100		-0.89

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: rs10081672;

hg19: chr9-35155908;