ENST00000654016.1:n.43+12576A>C

Variant names:

• chr6-90309585-A-C
• rs1394220
• ENST00000654016.1:n.43+12576A>C

Variant summary

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

The ENST00000654016.1(ENSG00000260271):​n.43+12576A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 152,044 control chromosomes in the GnomAD database, including 10,016 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 0.34 (10016 hom., cov: 32)
• Consequence: ENSG00000260271 ENST00000654016.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.587
• Publications: 8 publications found

Genes affected

ENSG00000260271 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377891	XR_007059677.1	n.498+11849A>C		intron_variant	Intron 1 of 4
LOC105377891	XR_942778.4	n.498+11849A>C		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000260271	ENST00000654016.1	n.43+12576A>C		intron_variant	Intron 1 of 7
ENSG00000260271	ENST00000663503.1	n.85+12576A>C		intron_variant	Intron 1 of 4
ENSG00000260271	ENST00000667364.1	n.30+14049A>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51842 AN: 151926 Hom.: 10011 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.378

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.341 AC: 51854 AN: 152044 Hom.: 10016 Cov.: 32 AF XY: 0.337 AC XY: 25072 AN XY: 74320

African (AFR) AF: 0.176 AC: 7303 AN: 41474

American (AMR) AF: 0.410 AC: 6269 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1778 AN: 3472

East Asian (EAS) AF: 0.135 AC: 699 AN: 5162

South Asian (SAS) AF: 0.362 AC: 1746 AN: 4820

European-Finnish (FIN) AF: 0.335 AC: 3539 AN: 10556

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.430 AC: 29224 AN: 67964

Other (OTH) AF: 0.374 AC: 791 AN: 2114

Alfa AF: 0.401 Hom.: 10095

Bravo AF: 0.339

Asia WGS AF: 0.250 AC: 871 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.5
DANN	Benign	0.72
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs1394220; hg19: chr6-91019304;