rs10496262

Positions:

• chr2-81524000-C-A

Variant summary

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

The XR_007088668.1(LOC102724542):​n.368-24618C>A 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 0.117 in 151,946 control chromosomes in the GnomAD database, including 1,325 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 0.12 (1325 hom., cov: 32)
• Consequence: LOC102724542 XR_007088668.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.684

Genes affected

LOC102724542 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102724542	XR_007088668.1	n.368-24618C>A		intron_variant, non_coding_transcript_variant
LOC102724542	XR_940294.2	n.368-24618C>A		intron_variant, non_coding_transcript_variant
LOC102724542	XR_940295.2	n.368-24618C>A		intron_variant, non_coding_transcript_variant
LOC102724542	XR_940298.2	n.368-24618C>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17711 AN: 151828 Hom.: 1325 Cov.: 32

Gnomad AFR AF: 0.0422

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.0796

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.00894

Gnomad SAS AF: 0.0458

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.0701

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.0997

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

GnomAD4 genome AF: 0.117 AC: 17709 AN: 151946 Hom.: 1325 Cov.: 32 AF XY: 0.113 AC XY: 8410 AN XY: 74252

Gnomad4 AFR AF: 0.0421

Gnomad4 AMR AF: 0.0795

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.00896

Gnomad4 SAS AF: 0.0459

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.0987

Alfa AF: 0.154 Hom.: 2191

Bravo AF: 0.107

Asia WGS AF: 0.0250 AC: 88 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.1
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10496262; hg19: chr2-81751124;