rs10509193

Positions:

• chr10-63678259-T-C

Variant summary

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

The XR_001747468.2(LOC107984238):​n.205+19829A>G 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 0.0676 in 152,292 control chromosomes in the GnomAD database, including 689 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 0.068 (689 hom., cov: 32)
• Consequence: LOC107984238 XR_001747468.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.433

Genes affected

LOC107984238 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107984238	XR_001747468.2	n.205+19829A>G		intron_variant, non_coding_transcript_variant
LOC124902438	XR_007062157.1	n.141-6663T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000444770.1	n.110-6663T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0674 AC: 10257 AN: 152174 Hom.: 683 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0337

Gnomad ASJ AF: 0.0277

Gnomad EAS AF: 0.0308

Gnomad SAS AF: 0.0313

Gnomad FIN AF: 0.0225

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0272

Gnomad OTH AF: 0.0478

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

GnomAD4 genome AF: 0.0676 AC: 10298 AN: 152292 Hom.: 689 Cov.: 32 AF XY: 0.0651 AC XY: 4851 AN XY: 74466

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.0336

Gnomad4 ASJ AF: 0.0277

Gnomad4 EAS AF: 0.0306

Gnomad4 SAS AF: 0.0313

Gnomad4 FIN AF: 0.0225

Gnomad4 NFE AF: 0.0271

Gnomad4 OTH AF: 0.0482

Alfa AF: 0.0482 Hom.: 52

Bravo AF: 0.0727

Asia WGS AF: 0.0340 AC: 117 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10509193; hg19: chr10-65438019;