rs10865170

Positions:

• chr2-41534660-C-A

Variant summary

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

The XR_939997.3(LOC105374506):​n.9529+3066G>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 0.326 in 151,974 control chromosomes in the GnomAD database, including 8,939 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 0.33 (8939 hom., cov: 32)
• Consequence: LOC105374506 XR_939997.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.148

Genes affected

LOC105374506 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374506	XR_939997.3	n.9529+3066G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49480 AN: 151856 Hom.: 8905 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.326 AC: 49549 AN: 151974 Hom.: 8939 Cov.: 32 AF XY: 0.332 AC XY: 24655 AN XY: 74282

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.460

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.719

Gnomad4 SAS AF: 0.345

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.325

Alfa AF: 0.294 Hom.: 861

Bravo AF: 0.340

Asia WGS AF: 0.529 AC: 1838 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10865170; hg19: chr2-41761800;