4-109882660-A-G

Variant names:

• chr4-109882660-A-G
• rs9685587
• ENST00000737086.1:n.174+4317T>C

Variant summary

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

The ENST00000737086.1(ENSG00000296171):​n.174+4317T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0686 in 152,282 control chromosomes in the GnomAD database, including 395 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 0.069 (395 hom., cov: 31)
• Consequence: ENSG00000296171 ENST00000737086.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230
• Publications: 1 publications found

Genes affected

ENSG00000296171 (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 = 0.175 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
ENSG00000296171	ENST00000737086.1	n.174+4317T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0685 AC: 10430 AN: 152164 Hom.: 393 Cov.: 31

Gnomad AFR AF: 0.0694

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.0813

Gnomad ASJ AF: 0.0806

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.0714

Gnomad FIN AF: 0.0496

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0579

Gnomad OTH AF: 0.0698

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

GnomAD4 genome AF: 0.0686 AC: 10451 AN: 152282 Hom.: 395 Cov.: 31 AF XY: 0.0703 AC XY: 5231 AN XY: 74460

African (AFR) AF: 0.0696 AC: 2893 AN: 41556

American (AMR) AF: 0.0809 AC: 1239 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0806 AC: 280 AN: 3472

East Asian (EAS) AF: 0.185 AC: 958 AN: 5176

South Asian (SAS) AF: 0.0719 AC: 347 AN: 4826

European-Finnish (FIN) AF: 0.0496 AC: 526 AN: 10614

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0579 AC: 3939 AN: 68010

Other (OTH) AF: 0.0738 AC: 156 AN: 2114

Alfa AF: 0.0631 Hom.: 1484

Bravo AF: 0.0709

Asia WGS AF: 0.127 AC: 442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.6
DANN	Benign	0.52
PhyloP100		0.023

Splicing

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

Other links and lift over

dbSNP: rs9685587; hg19: chr4-110803816;