14-65994169-G-T

Variant names:

• chr14-65994169-G-T
• rs1036979
• ENST00000554907.1:n.70-4426C>A

Variant summary

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

The ENST00000554907.1(ENSG00000258847):​n.70-4426C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 152,174 control chromosomes in the GnomAD database, including 4,123 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 0.19 (4123 hom., cov: 33)
• Consequence: ENSG00000258847 ENST00000554907.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.01
• Publications: 2 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=-0.7).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000554907.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000258847	ENST00000554907.1	TSL:2	n.70-4426C>A		intron	N/A
	ENSG00000258847	ENST00000775253.1		n.124-5519C>A		intron	N/A
	ENSG00000258847	ENST00000775254.1		n.123-5519C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28803 AN: 152056 Hom.: 4108 Cov.: 33

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.0763

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0848

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.190 AC: 28861 AN: 152174 Hom.: 4123 Cov.: 33 AF XY: 0.191 AC XY: 14214 AN XY: 74382

African (AFR) AF: 0.398 AC: 16496 AN: 41486

American (AMR) AF: 0.152 AC: 2330 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0763 AC: 265 AN: 3472

East Asian (EAS) AF: 0.210 AC: 1089 AN: 5184

South Asian (SAS) AF: 0.206 AC: 994 AN: 4828

European-Finnish (FIN) AF: 0.138 AC: 1463 AN: 10584

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0848 AC: 5766 AN: 68016

Other (OTH) AF: 0.144 AC: 305 AN: 2114

Alfa AF: 0.102 Hom.: 2230

Bravo AF: 0.197

Asia WGS AF: 0.217 AC: 758 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	12
DANN	Benign	0.57
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs1036979; hg19: chr14-66460887;