9-119878071-T-G

Variant names:

• chr9-119878071-T-G
• rs3934946
• ENST00000750211.1:n.102-3386A>C

Variant summary

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

The ENST00000750211.1(ENSG00000297691):​n.102-3386A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 152,170 control chromosomes in the GnomAD database, including 8,803 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 0.24 (8803 hom., cov: 32)
• Consequence: ENSG00000297691 ENST00000750211.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.110
• Publications: 2 publications found

Genes affected

ENSG00000297691 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000750211.1. 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
	ENSG00000297691	ENST00000750211.1		n.102-3386A>C		intron	N/A
	ENSG00000297691	ENST00000750212.1		n.184-3386A>C		intron	N/A
	ENSG00000297691	ENST00000750213.1		n.121-3386A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36478 AN: 152052 Hom.: 8767 Cov.: 32

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.0548

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0230

Gnomad FIN AF: 0.0671

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.240 AC: 36572 AN: 152170 Hom.: 8803 Cov.: 32 AF XY: 0.230 AC XY: 17116 AN XY: 74420

African (AFR) AF: 0.623 AC: 25840 AN: 41456

American (AMR) AF: 0.127 AC: 1947 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0548 AC: 190 AN: 3470

East Asian (EAS) AF: 0.00231 AC: 12 AN: 5188

South Asian (SAS) AF: 0.0230 AC: 111 AN: 4822

European-Finnish (FIN) AF: 0.0671 AC: 713 AN: 10624

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7209 AN: 67996

Other (OTH) AF: 0.197 AC: 417 AN: 2114

Alfa AF: 0.130 Hom.: 1098

Bravo AF: 0.263

Asia WGS AF: 0.0650 AC: 226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.74
PhyloP100		-0.11

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: rs3934946;

hg19: chr9-122640349;

COSMIC: COSV60400111;