14-65994169-G-T

Position:

• chr14-65994169-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000554907.1(ENSG00000258847):​n.70-4426C>A variant causes a intron, non coding transcript 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: ENST00000554907.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.01

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000554907.1	n.70-4426C>A		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.398

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.0763

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.0848

Gnomad4 OTH AF: 0.144

Alfa AF: 0.0919 Hom.: 1318

Bravo AF: 0.197

Asia WGS AF: 0.217 AC: 758 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1036979; hg19: chr14-66460887;