6-90319078-T-C

Variant names:

• chr6-90319078-T-C
• rs285640
• ENST00000654016.1:n.44-12286T>C

Variant summary

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

The ENST00000654016.1(ENSG00000260271):​n.44-12286T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 152,162 control chromosomes in the GnomAD database, including 7,934 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 0.29 (7934 hom., cov: 33)
• Consequence: ENSG00000260271 ENST00000654016.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.506
• Publications: 6 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377891	XR_007059677.1	n.498+21342T>C		intron_variant	Intron 1 of 4
LOC105377891	XR_942778.4	n.499-12286T>C		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000260271	ENST00000654016.1	n.44-12286T>C		intron_variant	Intron 1 of 7
ENSG00000260271	ENST00000663503.1	n.86-12286T>C		intron_variant	Intron 1 of 4
ENSG00000260271	ENST00000667364.1	n.30+23542T>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43563 AN: 152044 Hom.: 7938 Cov.: 33

Gnomad AFR AF: 0.0915

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.777

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.286 AC: 43566 AN: 152162 Hom.: 7934 Cov.: 33 AF XY: 0.296 AC XY: 22004 AN XY: 74360

African (AFR) AF: 0.0915 AC: 3802 AN: 41560

American (AMR) AF: 0.338 AC: 5169 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 905 AN: 3466

East Asian (EAS) AF: 0.776 AC: 4013 AN: 5170

South Asian (SAS) AF: 0.320 AC: 1544 AN: 4818

European-Finnish (FIN) AF: 0.460 AC: 4854 AN: 10554

Middle Eastern (MID) AF: 0.260 AC: 76 AN: 292

European-Non Finnish (NFE) AF: 0.329 AC: 22363 AN: 67992

Other (OTH) AF: 0.301 AC: 633 AN: 2106

Alfa AF: 0.299 Hom.: 14307

Bravo AF: 0.274

Asia WGS AF: 0.480 AC: 1666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.35
DANN	Benign	0.56
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs285640; hg19: chr6-91028797; COSMIC: COSV60243431;