rs4246861

Variant names:

• chr9-25599997-T-C
• rs4246861
• ENST00000754095.1:n.100-5695T>C

Variant summary

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

The ENST00000754095.1(ENSG00000298250):​n.100-5695T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 151,966 control chromosomes in the GnomAD database, including 7,737 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 0.30 (7737 hom., cov: 32)
• Consequence: ENSG00000298250 ENST00000754095.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.515
• Publications: 3 publications found

Genes affected

ENSG00000298250 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.452 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
ENSG00000298250	ENST00000754095.1	n.100-5695T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45116 AN: 151846 Hom.: 7718 Cov.: 32

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.297 AC: 45168 AN: 151966 Hom.: 7737 Cov.: 32 AF XY: 0.299 AC XY: 22201 AN XY: 74310

African (AFR) AF: 0.398 AC: 16508 AN: 41444

American (AMR) AF: 0.461 AC: 7037 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1062 AN: 3466

East Asian (EAS) AF: 0.425 AC: 2189 AN: 5152

South Asian (SAS) AF: 0.355 AC: 1707 AN: 4814

European-Finnish (FIN) AF: 0.149 AC: 1584 AN: 10600

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.204 AC: 13826 AN: 67936

Other (OTH) AF: 0.332 AC: 698 AN: 2100

Alfa AF: 0.238 Hom.: 13809

Bravo AF: 0.331

Asia WGS AF: 0.408 AC: 1418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.58
DANN	Benign	0.27
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs4246861; hg19: chr9-25599995;