9-5448690-G-C

Variant names:

• chr9-5448690-G-C
• rs822336
• ENST00000739687.1:n.104-723C>G

Variant summary

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

The ENST00000739687.1(ENSG00000296444):​n.104-723C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 152,062 control chromosomes in the GnomAD database, including 15,336 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 0.43 (15336 hom., cov: 32)
• Consequence: ENSG00000296444 ENST00000739687.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.212
• Publications: 31 publications found

Genes affected

ENSG00000296444 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296444	ENST00000739687.1	n.104-723C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.428 AC: 65106 AN: 151944 Hom.: 15329 Cov.: 32

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.428 AC: 65140 AN: 152062 Hom.: 15336 Cov.: 32 AF XY: 0.429 AC XY: 31916 AN XY: 74312

African (AFR) AF: 0.236 AC: 9785 AN: 41494

American (AMR) AF: 0.425 AC: 6492 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.513 AC: 1780 AN: 3472

East Asian (EAS) AF: 0.258 AC: 1334 AN: 5180

South Asian (SAS) AF: 0.461 AC: 2223 AN: 4820

European-Finnish (FIN) AF: 0.592 AC: 6249 AN: 10550

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.528 AC: 35845 AN: 67944

Other (OTH) AF: 0.466 AC: 983 AN: 2108

Alfa AF: 0.469 Hom.: 2155

Bravo AF: 0.405

Asia WGS AF: 0.375 AC: 1304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.48
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs822336; hg19: chr9-5448690; COSMIC: COSV67501138;