chr14-65355775-C-T

Variant names:

• chr14-65355775-C-T
• rs11621121
• ENST00000788187.1:n.132-19009C>T

Variant summary

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

The ENST00000788187.1(ENSG00000302621):​n.132-19009C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.434 in 151,874 control chromosomes in the GnomAD database, including 17,159 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 0.43 (17159 hom., cov: 31)
• Consequence: ENSG00000302621 ENST00000788187.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.353
• Publications: 6 publications found

Genes affected

ENSG00000302621 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.587 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
ENSG00000302621	ENST00000788187.1	n.132-19009C>T		intron_variant	Intron 1 of 4
ENSG00000302621	ENST00000788188.1	n.120-19009C>T		intron_variant	Intron 1 of 4
ENSG00000302621	ENST00000788189.1	n.147-19009C>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65857 AN: 151756 Hom.: 17157 Cov.: 31

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.434 AC: 65867 AN: 151874 Hom.: 17159 Cov.: 31 AF XY: 0.430 AC XY: 31897 AN XY: 74206

African (AFR) AF: 0.158 AC: 6533 AN: 41450

American (AMR) AF: 0.466 AC: 7099 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1747 AN: 3466

East Asian (EAS) AF: 0.195 AC: 1007 AN: 5168

South Asian (SAS) AF: 0.425 AC: 2037 AN: 4796

European-Finnish (FIN) AF: 0.539 AC: 5671 AN: 10528

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.592 AC: 40175 AN: 67906

Other (OTH) AF: 0.424 AC: 895 AN: 2110

Alfa AF: 0.526 Hom.: 42295

Bravo AF: 0.418

Asia WGS AF: 0.296 AC: 1030 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	4.9
DANN	Benign	0.78
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs11621121; hg19: chr14-65822493;