rs10490369

chr2-40955665-T-Cchr2-40955665-T-G

Variant summary

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

The XR_001739421.3(LOC105374497):n.59+14544A>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 0.0472 in 152,244 control chromosomes in the GnomAD database, including 633 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 0.047 (633 hom., cov: 32)
• Consequence: LOC105374497 XR_001739421.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.741

Genes affected

LOC105374497 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374497	XR_001739421.3	n.59+14544A>G		intron_variant, non_coding_transcript_variant
LOC105374497	XR_001739423.1	n.59+14544A>G		intron_variant, non_coding_transcript_variant
LOC105374497	XR_939994.2	n.59+14544A>G		intron_variant, non_coding_transcript_variant
LOC105374497	XR_939995.2	n.59+14544A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0472 AC: 7175 AN: 152126 Hom.: 627 Cov.: 32

Gnomad AFR AF: 0.00931

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.0585

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.0396

Gnomad FIN AF: 0.0427

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0207

Gnomad OTH AF: 0.0564

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

GnomAD4 genome AF: 0.0472 AC: 7182 AN: 152244 Hom.: 633 Cov.: 32 AF XY: 0.0524 AC XY: 3897 AN XY: 74426

Gnomad4 AFR AF: 0.00928

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.0585

Gnomad4 EAS AF: 0.275

Gnomad4 SAS AF: 0.0394

Gnomad4 FIN AF: 0.0427

Gnomad4 NFE AF: 0.0208

Gnomad4 OTH AF: 0.0553

Alfa AF: 0.0310 Hom.: 36

Bravo AF: 0.0622

Asia WGS AF: 0.141 AC: 489 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.37
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10490369; hg19: chr2-41182805;