14-102771441-G-A

Variant names:

• chr14-102771441-G-A
• rs7143468
• ENST00000559402.2:n.305C>T

Variant summary

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

The ENST00000559402.2(ENSG00000259508):​n.305C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 152,202 control chromosomes in the GnomAD database, including 19,473 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 0.47 (19471 hom., cov: 32)
  • Exomes 𝑓: 0.21 (2 hom.)
• Consequence: ENSG00000259508 ENST00000559402.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86
• Publications: 4 publications found

Genes affected

ENSG00000259508 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000559402.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259508	ENST00000559402.2	TSL:4	n.305C>T		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000259508	ENST00000559675.1	TSL:4	n.152-986C>T		intron	N/A
	ENSG00000259508	ENST00000828087.1		n.376-986C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71141 AN: 151946 Hom.: 19433 Cov.: 32

Gnomad AFR AF: 0.765

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.435

GnomAD4 exome AF: 0.210 AC: 29 AN: 138 Hom.: 2 Cov.: 0 AF XY: 0.179 AC XY: 20 AN XY: 112

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.500 AC: 2 AN: 4

South Asian (SAS) AF: 0.125 AC: 1 AN: 8

European-Finnish (FIN) AF: 0.250 AC: 3 AN: 12

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.200 AC: 20 AN: 100

Other (OTH) AF: 0.200 AC: 2 AN: 10

GnomAD4 genome AF: 0.469 AC: 71246 AN: 152064 Hom.: 19471 Cov.: 32 AF XY: 0.468 AC XY: 34761 AN XY: 74328

African (AFR) AF: 0.765 AC: 31731 AN: 41470

American (AMR) AF: 0.427 AC: 6524 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1243 AN: 3468

East Asian (EAS) AF: 0.517 AC: 2665 AN: 5158

South Asian (SAS) AF: 0.329 AC: 1586 AN: 4822

European-Finnish (FIN) AF: 0.391 AC: 4127 AN: 10562

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.325 AC: 22069 AN: 67992

Other (OTH) AF: 0.435 AC: 918 AN: 2108

Alfa AF: 0.375 Hom.: 30173

Bravo AF: 0.491

Asia WGS AF: 0.475 AC: 1647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.022
DANN	Benign	0.86
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs7143468; hg19: chr14-103237778;