rs9630112

chr10-88084818-T-Achr10-88084818-T-Cchr10-88084818-T-G

Variant summary

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

The XR_007062225.1(LOC105378415):n.264+431A>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 152,062 control chromosomes in the GnomAD database, including 22,800 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 0.52 (22800 hom., cov: 32)
• Consequence: LOC105378415 XR_007062225.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.303

Genes affected

LOC105378415 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378415	XR_007062225.1	n.264+431A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78790 AN: 151942 Hom.: 22759 Cov.: 32

Gnomad AFR AF: 0.791

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.519 AC: 78883 AN: 152062 Hom.: 22800 Cov.: 32 AF XY: 0.511 AC XY: 38017 AN XY: 74342

Gnomad4 AFR AF: 0.791

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.421

Gnomad4 NFE AF: 0.418

Gnomad4 OTH AF: 0.527

Alfa AF: 0.265 Hom.: 533

Bravo AF: 0.532

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.083
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9630112; hg19: chr10-89844575;