rs710285

Variant names:

• chr14-98068349-A-G
• rs710285
• ENST00000555776.1:n.433T>C

Variant summary

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

The ENST00000555776.1(ENSG00000259097):​n.433T>C 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 0.413 in 152,032 control chromosomes in the GnomAD database, including 13,116 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 0.41 (13113 hom., cov: 32)
  • Exomes 𝑓: 0.57 (3 hom.)
• Consequence: ENSG00000259097 ENST00000555776.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.46
• Publications: 5 publications found

Genes affected

ENSG00000259097 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000555776.1. 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
	ENSG00000259097	ENST00000555776.1	TSL:4	n.433T>C		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000259097	ENST00000663808.2		n.517T>C		non_coding_transcript_exon	Exon 4 of 4
	ENSG00000259097	ENST00000835632.1		n.263T>C		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62794 AN: 151900 Hom.: 13099 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.438

GnomAD4 exome AF: 0.571 AC: 8 AN: 14 Hom.: 3 Cov.: 0 AF XY: 0.700 AC XY: 7 AN XY: 10

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.583 AC: 7 AN: 12

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.413 AC: 62850 AN: 152018 Hom.: 13113 Cov.: 32 AF XY: 0.412 AC XY: 30594 AN XY: 74318

African (AFR) AF: 0.373 AC: 15451 AN: 41454

American (AMR) AF: 0.478 AC: 7302 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1356 AN: 3472

East Asian (EAS) AF: 0.358 AC: 1850 AN: 5164

South Asian (SAS) AF: 0.363 AC: 1749 AN: 4816

European-Finnish (FIN) AF: 0.420 AC: 4435 AN: 10564

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.431 AC: 29288 AN: 67966

Other (OTH) AF: 0.439 AC: 927 AN: 2110

Alfa AF: 0.422 Hom.: 7669

Bravo AF: 0.419

Asia WGS AF: 0.350 AC: 1219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.030
DANN	Benign	0.31
PhyloP100		-4.5

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs710285;

hg19: chr14-98534686;