rs4899260

Variant names:

• chr14-68811487-C-T
• rs4899260
• ENST00000780276.1:n.298+4665G>A

Variant summary

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

The ENST00000780276.1(ENSG00000301622):​n.298+4665G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 152,166 control chromosomes in the GnomAD database, including 6,339 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 0.27 (6339 hom., cov: 33)
• Consequence: ENSG00000301622 ENST00000780276.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 16 publications found

Genes affected

ENSG00000301622 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.38 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
ENSG00000301622	ENST00000780276.1	n.298+4665G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41317 AN: 152048 Hom.: 6336 Cov.: 33

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.272 AC: 41339 AN: 152166 Hom.: 6339 Cov.: 33 AF XY: 0.265 AC XY: 19685 AN XY: 74404

African (AFR) AF: 0.385 AC: 15949 AN: 41472

American (AMR) AF: 0.199 AC: 3046 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 861 AN: 3468

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5182

South Asian (SAS) AF: 0.187 AC: 902 AN: 4826

European-Finnish (FIN) AF: 0.224 AC: 2375 AN: 10608

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.255 AC: 17363 AN: 67992

Other (OTH) AF: 0.250 AC: 530 AN: 2116

Alfa AF: 0.258 Hom.: 13325

Bravo AF: 0.274

Asia WGS AF: 0.104 AC: 365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.9
DANN	Benign	0.68
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs4899260; hg19: chr14-69278204;