rs2503875

Positions:

• chr10-43318601-G-A
• chr10-43318601-G-T

Variant summary

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

The XR_945902.3(LOC105378271):​n.198+6G>A variant causes a splice donor region, intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 152,162 control chromosomes in the GnomAD database, including 5,582 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 0.24 (5582 hom., cov: 32)
• Consequence: LOC105378271 XR_945902.3 splice_donor_region, intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97

Genes affected

LOC105378271 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378271	XR_945902.3	n.198+6G>A		splice_donor_region_variant, intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37149 AN: 152044 Hom.: 5584 Cov.: 32

Gnomad AFR AF: 0.0696

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.244 AC: 37148 AN: 152162 Hom.: 5582 Cov.: 32 AF XY: 0.248 AC XY: 18466 AN XY: 74390

Gnomad4 AFR AF: 0.0696

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.251

Alfa AF: 0.292 Hom.: 15084

Bravo AF: 0.236

Asia WGS AF: 0.385 AC: 1335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.050
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2503875; hg19: chr10-43814049;