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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000728943.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295274	ENST00000728943.1		n.265-30195C>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2217448;

hg19: chr14-82510077;