4-111002885-C-T

Variant names:

• chr4-111002885-C-T
• rs9307358
• ENST00000681682.2:n.493+88767C>T

Variant summary

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

The ENST00000681682.2(ENSG00000288692):​n.493+88767C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,088 control chromosomes in the GnomAD database, including 5,433 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 0.16 (5433 hom., cov: 32)
• Consequence: ENSG00000288692 ENST00000681682.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.101
• Publications: 2 publications found

Genes affected

ENSG00000288692 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377364	XR_001741518.2	n.145-560G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288692	ENST00000681682.2	n.493+88767C>T		intron_variant	Intron 2 of 5
ENSG00000309167	ENST00000839195.1	n.185-560G>A		intron_variant	Intron 2 of 4
ENSG00000309167	ENST00000839196.1	n.183-560G>A		intron_variant	Intron 2 of 5
ENSG00000309167	ENST00000839198.1	n.169-560G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24926 AN: 151972 Hom.: 5406 Cov.: 32

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0636

Gnomad ASJ AF: 0.0225

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.0939

Gnomad FIN AF: 0.0245

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0163

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.164 AC: 24994 AN: 152088 Hom.: 5433 Cov.: 32 AF XY: 0.162 AC XY: 12068 AN XY: 74364

African (AFR) AF: 0.494 AC: 20436 AN: 41400

American (AMR) AF: 0.0634 AC: 970 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0225 AC: 78 AN: 3470

East Asian (EAS) AF: 0.267 AC: 1382 AN: 5168

South Asian (SAS) AF: 0.0938 AC: 452 AN: 4818

European-Finnish (FIN) AF: 0.0245 AC: 260 AN: 10602

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0163 AC: 1110 AN: 68014

Other (OTH) AF: 0.135 AC: 286 AN: 2114

Alfa AF: 0.0514 Hom.: 1483

Bravo AF: 0.182

Asia WGS AF: 0.205 AC: 713 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.2
DANN	Benign	0.45
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs9307358; hg19: chr4-111924041;