10-114029616-C-T

Variant names:

• chr10-114029616-C-T
• rs7076938
• XR_946333.3:n.391-1211C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_946333.3(LOC105378493):​n.391-1211C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.696 in 152,046 control chromosomes in the GnomAD database, including 37,211 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 0.70 (37211 hom., cov: 31)
• Consequence: LOC105378493 XR_946333.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0380

Genes affected

LOC105378493 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378493	XR_946333.3	n.391-1211C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.696 AC: 105703 AN: 151928 Hom.: 37169 Cov.: 31

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.619

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.762

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.746

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.729

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.696 AC: 105803 AN: 152046 Hom.: 37211 Cov.: 31 AF XY: 0.699 AC XY: 51944 AN XY: 74308

Gnomad4 AFR AF: 0.600

Gnomad4 AMR AF: 0.767

Gnomad4 ASJ AF: 0.615

Gnomad4 EAS AF: 0.762

Gnomad4 SAS AF: 0.743

Gnomad4 FIN AF: 0.746

Gnomad4 NFE AF: 0.729

Gnomad4 OTH AF: 0.671

Alfa AF: 0.717 Hom.: 46206

Bravo AF: 0.691

Asia WGS AF: 0.728 AC: 2530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.0
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7076938; hg19: chr10-115789375;