14-102771171-T-C

Variant names:

• chr14-102771171-T-C
• rs10131139
• ENST00000559402.2:n.575A>G

Variant summary

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

The ENST00000559402.2(ENSG00000259508):​n.575A>G 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 0.248 in 152,328 control chromosomes in the GnomAD database, including 4,858 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 0.25 (4853 hom., cov: 33)
  • Exomes 𝑓: 0.33 (5 hom.)
• Consequence: ENSG00000259508 ENST00000559402.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.492
• Publications: 5 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.443 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259508	ENST00000559402.2	TSL:4	n.575A>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000259508	ENST00000559675.1	TSL:4	n.152-716A>G		intron	N/A
	ENSG00000259508	ENST00000828087.1		n.376-716A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37651 AN: 152144 Hom.: 4843 Cov.: 33

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.243

GnomAD4 exome AF: 0.333 AC: 22 AN: 66 Hom.: 5 Cov.: 0 AF XY: 0.354 AC XY: 17 AN XY: 48

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.00 AC: 0 AN: 6

European-Finnish (FIN) AF: 0.250 AC: 1 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.380 AC: 19 AN: 50

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.248 AC: 37695 AN: 152262 Hom.: 4853 Cov.: 33 AF XY: 0.246 AC XY: 18346 AN XY: 74450

African (AFR) AF: 0.275 AC: 11421 AN: 41538

American (AMR) AF: 0.248 AC: 3796 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 633 AN: 3470

East Asian (EAS) AF: 0.458 AC: 2373 AN: 5176

South Asian (SAS) AF: 0.274 AC: 1322 AN: 4830

European-Finnish (FIN) AF: 0.207 AC: 2193 AN: 10612

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15184 AN: 68012

Other (OTH) AF: 0.244 AC: 516 AN: 2114

Alfa AF: 0.235 Hom.: 1967

Bravo AF: 0.257

Asia WGS AF: 0.319 AC: 1112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.54
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs10131139; hg19: chr14-103237508;