rs10496382

Positions:

• chr2-104120276-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_923128.1(LOC105373523):​n.537+4864G>A variant causes a intron, non coding transcript change. The variant allele was found at a frequency of 0.0683 in 152,152 control chromosomes in the GnomAD database, including 386 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 (386 hom., cov: 32)
• Consequence: LOC105373523 XR_923128.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.60

Genes affected

LOC105373523 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.19).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0855 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373523	XR_923128.1	n.537+4864G>A		intron_variant, non_coding_transcript_variant
LOC105373523	XR_923127.1	n.541+4864G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0683 AC: 10380 AN: 152034 Hom.: 385 Cov.: 32

Gnomad AFR AF: 0.0878

Gnomad AMI AF: 0.0505

Gnomad AMR AF: 0.0586

Gnomad ASJ AF: 0.0838

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0757

Gnomad FIN AF: 0.0970

Gnomad MID AF: 0.0701

Gnomad NFE AF: 0.0579

Gnomad OTH AF: 0.0747

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

GnomAD4 genome AF: 0.0683 AC: 10388 AN: 152152 Hom.: 386 Cov.: 32 AF XY: 0.0688 AC XY: 5115 AN XY: 74370

Gnomad4 AFR AF: 0.0878

Gnomad4 AMR AF: 0.0583

Gnomad4 ASJ AF: 0.0838

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0762

Gnomad4 FIN AF: 0.0970

Gnomad4 NFE AF: 0.0579

Gnomad4 OTH AF: 0.0739

Alfa AF: 0.0614 Hom.: 336

Bravo AF: 0.0654

Asia WGS AF: 0.0380 AC: 133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.19
CADD	Benign	20
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10496382; hg19: chr2-104736734;