ENST00000641725.1:n.100C>A

Variant names:

• chr14-64386954-G-T
• rs4243628
• ENST00000641725.1:n.100C>A

Variant summary

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

The ENST00000641725.1(ENSG00000293482):​n.100C>A 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 0.375 in 152,154 control chromosomes in the GnomAD database, including 13,166 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 0.38 (13158 hom., cov: 33)
  • Exomes 𝑓: 0.56 (8 hom.)
• Consequence: ENSG00000293482 ENST00000641725.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.243
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.486 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.100C>A		non_coding_transcript_exon_variant	Exon 1 of 6
ENSG00000293482	ENST00000689962.2	n.1026C>A		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000293482	ENST00000641479.1	n.570+463C>A		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.375 AC: 57050 AN: 151986 Hom.: 13158 Cov.: 33

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.567

Gnomad MID AF: 0.442

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.395

GnomAD4 exome AF: 0.560 AC: 28 AN: 50 Hom.: 8 Cov.: 0 AF XY: 0.595 AC XY: 25 AN XY: 42

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

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

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

European-Non Finnish (NFE) AF: 0.625 AC: 25 AN: 40

Other (OTH) AF: 1.00 AC: 2 AN: 2

GnomAD4 genome AF: 0.375 AC: 57059 AN: 152104 Hom.: 13158 Cov.: 33 AF XY: 0.383 AC XY: 28449 AN XY: 74356

African (AFR) AF: 0.100 AC: 4153 AN: 41520

American (AMR) AF: 0.467 AC: 7139 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1373 AN: 3470

East Asian (EAS) AF: 0.281 AC: 1449 AN: 5154

South Asian (SAS) AF: 0.467 AC: 2256 AN: 4826

European-Finnish (FIN) AF: 0.567 AC: 6006 AN: 10594

Middle Eastern (MID) AF: 0.459 AC: 133 AN: 290

European-Non Finnish (NFE) AF: 0.491 AC: 33354 AN: 67962

Other (OTH) AF: 0.397 AC: 837 AN: 2108

Alfa AF: 0.435 Hom.: 2000

Bravo AF: 0.355

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.4
DANN	Benign	0.83
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs4243628; hg19: chr14-64853672;