14-26965634-T-C

Position:

• chr14-26965634-T-C

Variant summary

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

The ENST00000656336.1(ENSG00000258081):​n.481-168336T>C 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 0.883 in 152,182 control chromosomes in the GnomAD database, including 60,081 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 0.88 (60081 hom., cov: 32)
• Consequence: ENST00000656336.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370419	XR_001750688.1	n.1940-1574T>C		intron_variant, non_coding_transcript_variant
LOC105370419	XR_001750687.1	n.427-1574T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000656336.1	n.481-168336T>C		intron_variant, non_coding_transcript_variant
	ENST00000552303.1	n.206-111604T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.884 AC: 134353 AN: 152064 Hom.: 60042 Cov.: 32

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.963

Gnomad AMR AF: 0.936

Gnomad ASJ AF: 0.943

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.892

Gnomad FIN AF: 0.959

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.938

Gnomad OTH AF: 0.902

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

GnomAD4 genome AF: 0.883 AC: 134446 AN: 152182 Hom.: 60081 Cov.: 32 AF XY: 0.885 AC XY: 65884 AN XY: 74426

Gnomad4 AFR AF: 0.732

Gnomad4 AMR AF: 0.937

Gnomad4 ASJ AF: 0.943

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.891

Gnomad4 FIN AF: 0.959

Gnomad4 NFE AF: 0.938

Gnomad4 OTH AF: 0.904

Alfa AF: 0.906 Hom.: 7811

Bravo AF: 0.877

Asia WGS AF: 0.951 AC: 3308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4328361; hg19: chr14-27434840;