rs2250266

chr10-121138399-G-A

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The XR_946379.3(LOC105378522):n.356+8576G>A variant causes a intron, non coding transcript change. The variant allele was found at a frequency of 0.488 in 152,080 control chromosomes in the GnomAD database, including 20,507 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.49 (20507 hom., cov: 32)
• Consequence: LOC105378522 XR_946379.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.07

Genes affected

LOC124902515 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902515	XR_007062318.1	n.159-19050C>T		intron_variant, non_coding_transcript_variant
LOC105378522	XR_946379.3	n.356+8576G>A		intron_variant, non_coding_transcript_variant
LOC124902515	XR_007062317.1	n.168-19050C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74205 AN: 151962 Hom.: 20508 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.759

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.488 AC: 74228 AN: 152080 Hom.: 20507 Cov.: 32 AF XY: 0.489 AC XY: 36364 AN XY: 74324

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.459

Gnomad4 ASJ AF: 0.634

Gnomad4 EAS AF: 0.378

Gnomad4 SAS AF: 0.760

Gnomad4 FIN AF: 0.615

Gnomad4 NFE AF: 0.609

Gnomad4 OTH AF: 0.516

Alfa AF: 0.594 Hom.: 38853

Bravo AF: 0.455

Asia WGS AF: 0.531 AC: 1845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Uncertain	-0.070
Cadd	Benign	21
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: rs2250266; hg19: chr10-122897913;