chr9-120018976-T-G

Variant names:

• chr9-120018976-T-G
• rs2416745
• ENST00000765277.1:n.238-550A>C

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The ENST00000765277.1(ENSG00000299636):​n.238-550A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,228 control chromosomes in the GnomAD database, including 2,269 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 0.15 (2269 hom., cov: 33)
• Consequence: ENSG00000299636 ENST00000765277.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.96
• Publications: 4 publications found

Genes affected

ENSG00000299636 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.13).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000765277.1. 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
	ENSG00000299636	ENST00000765277.1		n.238-550A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22944 AN: 152110 Hom.: 2267 Cov.: 33

Gnomad AFR AF: 0.0443

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.151 AC: 22948 AN: 152228 Hom.: 2269 Cov.: 33 AF XY: 0.155 AC XY: 11541 AN XY: 74416

African (AFR) AF: 0.0443 AC: 1840 AN: 41566

American (AMR) AF: 0.140 AC: 2144 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 705 AN: 3470

East Asian (EAS) AF: 0.319 AC: 1655 AN: 5180

South Asian (SAS) AF: 0.360 AC: 1732 AN: 4816

European-Finnish (FIN) AF: 0.159 AC: 1680 AN: 10586

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12434 AN: 67998

Other (OTH) AF: 0.169 AC: 356 AN: 2108

Alfa AF: 0.182 Hom.: 2062

Bravo AF: 0.139

Asia WGS AF: 0.262 AC: 911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.13
CADD	Benign	21
DANN	Benign	0.92
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: rs2416745;

hg19: chr9-122781254;