rs10507988

Variant names:

• chr13-90890370-C-T
• rs10507988
• XR_931637.2:n.748+1860C>T

Variant summary

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

The XR_931637.2(LOC105370311):​n.748+1860C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0542 in 152,228 control chromosomes in the GnomAD database, including 465 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 0.054 (465 hom., cov: 32)
• Consequence: LOC105370311 XR_931637.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.388
• Publications: 2 publications found

Genes affected

LOC105370311 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0541 AC: 8229 AN: 152110 Hom.: 460 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0415

Gnomad ASJ AF: 0.0395

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00621

Gnomad FIN AF: 0.00773

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0192

Gnomad OTH AF: 0.0440

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

GnomAD4 genome AF: 0.0542 AC: 8257 AN: 152228 Hom.: 465 Cov.: 32 AF XY: 0.0531 AC XY: 3950 AN XY: 74438

African (AFR) AF: 0.144 AC: 5967 AN: 41524

American (AMR) AF: 0.0414 AC: 633 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0395 AC: 137 AN: 3466

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5182

South Asian (SAS) AF: 0.00622 AC: 30 AN: 4824

European-Finnish (FIN) AF: 0.00773 AC: 82 AN: 10608

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0192 AC: 1305 AN: 68016

Other (OTH) AF: 0.0435 AC: 92 AN: 2114

Alfa AF: 0.0375 Hom.: 46

Bravo AF: 0.0601

Asia WGS AF: 0.0150 AC: 53 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.7
DANN	Benign	0.77
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs10507988; hg19: chr13-91542624;