rs17103248

Variant names:

• chr14-66049950-G-A
• rs17103248
• ENST00000775253.1:n.124-61300C>T

Variant summary

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

The ENST00000775253.1(ENSG00000258847):​n.124-61300C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 152,076 control chromosomes in the GnomAD database, including 4,370 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 0.24 (4370 hom., cov: 32)
• Consequence: ENSG00000258847 ENST00000775253.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0480
• Publications: 3 publications found

Genes affected

ENSG00000258847 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.312 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
ENSG00000258847	ENST00000775253.1	n.124-61300C>T		intron_variant	Intron 1 of 3
ENSG00000258847	ENST00000775254.1	n.123-61300C>T		intron_variant	Intron 1 of 2
ENSG00000258847	ENST00000775255.1	n.123-10390C>T		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.237 AC: 35991 AN: 151958 Hom.: 4366 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.237 AC: 36022 AN: 152076 Hom.: 4370 Cov.: 32 AF XY: 0.239 AC XY: 17750 AN XY: 74330

African (AFR) AF: 0.249 AC: 10306 AN: 41464

American (AMR) AF: 0.217 AC: 3316 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 707 AN: 3470

East Asian (EAS) AF: 0.269 AC: 1392 AN: 5166

South Asian (SAS) AF: 0.325 AC: 1565 AN: 4814

European-Finnish (FIN) AF: 0.265 AC: 2804 AN: 10564

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15252 AN: 67986

Other (OTH) AF: 0.215 AC: 454 AN: 2114

Alfa AF: 0.233 Hom.: 2316

Bravo AF: 0.230

Asia WGS AF: 0.299 AC: 1038 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.3
DANN	Benign	0.69
PhyloP100		0.048

Splicing

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

Other links and lift over

dbSNP: rs17103248; hg19: chr14-66516668;