ENST00000641725.1:n.96T>C

Variant names:

• chr14-64386958-A-G
• rs8010584
• ENST00000641725.1:n.96T>C

Variant summary

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

The ENST00000641725.1(ENSG00000293482):​n.96T>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 0.553 in 152,110 control chromosomes in the GnomAD database, including 25,780 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 0.55 (25777 hom., cov: 32)
  • Exomes 𝑓: 0.40 (3 hom.)
• Consequence: ENSG00000293482 ENST00000641725.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.847
• Publications: 5 publications found

Genes affected

ENSG00000293482 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.826 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293482	ENST00000641725.1	n.96T>C		non_coding_transcript_exon_variant	Exon 1 of 6
ENSG00000293482	ENST00000689962.2	n.1022T>C		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000293482	ENST00000641479.1	n.570+459T>C		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.553 AC: 84077 AN: 151942 Hom.: 25738 Cov.: 32

Gnomad AFR AF: 0.834

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.541

GnomAD4 exome AF: 0.400 AC: 20 AN: 50 Hom.: 3 Cov.: 0 AF XY: 0.405 AC XY: 17 AN XY: 42

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AC: 0 AN: 0

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

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.381 AC: 16 AN: 42

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

GnomAD4 genome AF: 0.554 AC: 84171 AN: 152060 Hom.: 25777 Cov.: 32 AF XY: 0.544 AC XY: 40407 AN XY: 74322

African (AFR) AF: 0.834 AC: 34596 AN: 41496

American (AMR) AF: 0.477 AC: 7282 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.563 AC: 1953 AN: 3468

East Asian (EAS) AF: 0.363 AC: 1873 AN: 5158

South Asian (SAS) AF: 0.489 AC: 2356 AN: 4816

European-Finnish (FIN) AF: 0.340 AC: 3599 AN: 10580

Middle Eastern (MID) AF: 0.531 AC: 155 AN: 292

European-Non Finnish (NFE) AF: 0.452 AC: 30702 AN: 67956

Other (OTH) AF: 0.535 AC: 1130 AN: 2112

Alfa AF: 0.341 Hom.: 904

Bravo AF: 0.576

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.6
DANN	Benign	0.60
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs8010584; hg19: chr14-64853676;