rs10507451

Variant names:

• chr13-37303389-T-A
• rs10507451
• ENST00000827668.1:n.233-3963T>A

Variant summary

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

The ENST00000827668.1(ENSG00000307651):​n.233-3963T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.031 in 152,318 control chromosomes in the GnomAD database, including 173 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 0.031 (173 hom., cov: 32)
• Consequence: ENSG00000307651 ENST00000827668.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.249
• Publications: 0 publications found

Genes affected

ENSG00000307651 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.077 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
ENSG00000307651	ENST00000827668.1	n.233-3963T>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0310 AC: 4715 AN: 152200 Hom.: 173 Cov.: 32

Gnomad AFR AF: 0.0793

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0173

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.0612

Gnomad SAS AF: 0.0588

Gnomad FIN AF: 0.0114

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.00401

Gnomad OTH AF: 0.0297

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

GnomAD4 genome AF: 0.0310 AC: 4727 AN: 152318 Hom.: 173 Cov.: 32 AF XY: 0.0311 AC XY: 2317 AN XY: 74482

African (AFR) AF: 0.0793 AC: 3295 AN: 41568

American (AMR) AF: 0.0172 AC: 263 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0239 AC: 83 AN: 3470

East Asian (EAS) AF: 0.0612 AC: 317 AN: 5182

South Asian (SAS) AF: 0.0595 AC: 287 AN: 4826

European-Finnish (FIN) AF: 0.0114 AC: 121 AN: 10622

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.00401 AC: 273 AN: 68028

Other (OTH) AF: 0.0322 AC: 68 AN: 2112

Alfa AF: 0.0202 Hom.: 17

Bravo AF: 0.0319

Asia WGS AF: 0.0710 AC: 247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.39
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs10507451; hg19: chr13-37877526;