14-84118944-C-T

Variant names:

• chr14-84118944-C-T
• rs1676060
• ENST00000649337.1:n.185+21416G>A

Variant summary

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

The ENST00000649337.1(ENSG00000285826):​n.185+21416G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.964 in 152,178 control chromosomes in the GnomAD database, including 71,078 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 0.96 (71078 hom., cov: 32)
• Consequence: ENSG00000285826 ENST00000649337.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81
• Publications: 0 publications found

Genes affected

ENSG00000285826 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.987 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
ENSG00000285826	ENST00000649337.1	n.185+21416G>A		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.964 AC: 146635 AN: 152060 Hom.: 71030 Cov.: 32

Gnomad AFR AF: 0.995

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.895

Gnomad ASJ AF: 0.988

Gnomad EAS AF: 0.669

Gnomad SAS AF: 0.955

Gnomad FIN AF: 0.967

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.982

Gnomad OTH AF: 0.964

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

GnomAD4 genome AF: 0.964 AC: 146739 AN: 152178 Hom.: 71078 Cov.: 32 AF XY: 0.960 AC XY: 71442 AN XY: 74402

African (AFR) AF: 0.995 AC: 41345 AN: 41562

American (AMR) AF: 0.895 AC: 13659 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.988 AC: 3427 AN: 3468

East Asian (EAS) AF: 0.669 AC: 3445 AN: 5146

South Asian (SAS) AF: 0.955 AC: 4610 AN: 4826

European-Finnish (FIN) AF: 0.967 AC: 10263 AN: 10616

Middle Eastern (MID) AF: 0.973 AC: 286 AN: 294

European-Non Finnish (NFE) AF: 0.982 AC: 66769 AN: 67982

Other (OTH) AF: 0.957 AC: 2023 AN: 2114

Alfa AF: 0.971 Hom.: 3341

Bravo AF: 0.958

Asia WGS AF: 0.820 AC: 2852 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	0.13
DANN	Benign	0.50
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1676060; hg19: chr14-84585288;