rs2217448

Variant names:

• chr14-82043733-C-T
• rs2217448
• ENST00000728943.1:n.265-30195C>T

Variant summary

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

The ENST00000728943.1(ENSG00000295274):​n.265-30195C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 151,682 control chromosomes in the GnomAD database, including 1,147 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 0.11 (1147 hom., cov: 32)
• Consequence: ENSG00000295274 ENST00000728943.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.180
• Publications: 3 publications found

Genes affected

ENSG00000295274 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984704	XR_007064292.1	n.842-30195C>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295274	ENST00000728943.1	n.265-30195C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16663 AN: 151564 Hom.: 1147 Cov.: 32

Gnomad AFR AF: 0.0293

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.110 AC: 16651 AN: 151682 Hom.: 1147 Cov.: 32 AF XY: 0.109 AC XY: 8049 AN XY: 74076

African (AFR) AF: 0.0291 AC: 1206 AN: 41388

American (AMR) AF: 0.101 AC: 1544 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 618 AN: 3470

East Asian (EAS) AF: 0.206 AC: 1062 AN: 5148

South Asian (SAS) AF: 0.120 AC: 574 AN: 4790

European-Finnish (FIN) AF: 0.118 AC: 1235 AN: 10470

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9933 AN: 67868

Other (OTH) AF: 0.124 AC: 261 AN: 2110

Alfa AF: 0.134 Hom.: 2736

Bravo AF: 0.105

Asia WGS AF: 0.137 AC: 475 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.9
DANN	Benign	0.81
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs2217448; hg19: chr14-82510077;