rs6481257

Variant names:

• chr10-57178792-C-A
• rs6481257
• ENST00000690550.2:n.146+43820G>T

Variant summary

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

The ENST00000690550.2(ENSG00000289158):​n.146+43820G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 151,704 control chromosomes in the GnomAD database, including 19,608 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 0.45 (19608 hom., cov: 31)
• Consequence: ENSG00000289158 ENST00000690550.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.442
• Publications: 5 publications found

Genes affected

ENSG00000289158 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.816 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
ENSG00000289158	ENST00000690550.2	n.146+43820G>T		intron_variant	Intron 1 of 2
ENSG00000289158	ENST00000752897.1	n.151+43820G>T		intron_variant	Intron 1 of 3
ENSG00000289158	ENST00000752899.1	n.67-38582G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68181 AN: 151586 Hom.: 19559 Cov.: 31

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.450 AC: 68286 AN: 151704 Hom.: 19608 Cov.: 31 AF XY: 0.447 AC XY: 33123 AN XY: 74084

African (AFR) AF: 0.823 AC: 34052 AN: 41380

American (AMR) AF: 0.340 AC: 5180 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 726 AN: 3462

East Asian (EAS) AF: 0.168 AC: 864 AN: 5144

South Asian (SAS) AF: 0.401 AC: 1930 AN: 4818

European-Finnish (FIN) AF: 0.328 AC: 3426 AN: 10450

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20737 AN: 67922

Other (OTH) AF: 0.424 AC: 890 AN: 2098

Alfa AF: 0.337 Hom.: 37598

Bravo AF: 0.468

Asia WGS AF: 0.365 AC: 1267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.71
DANN	Benign	0.21
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs6481257; hg19: chr10-58938552;