rs28788874

Variant names:

• chr1-1585345-C-T
• rs28788874
• ENST00000763257.1:n.247-6760C>T

Variant summary

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

The ENST00000763257.1(ENSG00000299413):​n.247-6760C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 151,772 control chromosomes in the GnomAD database, including 8,249 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 (8249 hom., cov: 32)
• Consequence: ENSG00000299413 ENST00000763257.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.70
• Publications: 1 publications found

Genes affected

ENSG00000299413 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.406 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
ENSG00000299413	ENST00000763257.1	n.247-6760C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.303 AC: 45989 AN: 151654 Hom.: 8249 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.303 AC: 45983 AN: 151772 Hom.: 8249 Cov.: 32 AF XY: 0.299 AC XY: 22163 AN XY: 74150

African (AFR) AF: 0.126 AC: 5200 AN: 41378

American (AMR) AF: 0.270 AC: 4111 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1663 AN: 3466

East Asian (EAS) AF: 0.143 AC: 735 AN: 5156

South Asian (SAS) AF: 0.250 AC: 1198 AN: 4792

European-Finnish (FIN) AF: 0.373 AC: 3923 AN: 10524

Middle Eastern (MID) AF: 0.449 AC: 131 AN: 292

European-Non Finnish (NFE) AF: 0.410 AC: 27827 AN: 67916

Other (OTH) AF: 0.345 AC: 725 AN: 2100

Alfa AF: 0.334 Hom.: 1189

Bravo AF: 0.287

Asia WGS AF: 0.203 AC: 707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.24
DANN	Benign	0.55
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs28788874; hg19: chr1-1520725;