rs10795055

Positions:

• chr10-3539029-A-G

Variant summary

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

The NR_131187.1(LOC105376360):​n.163-209659A>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 0.537 in 152,044 control chromosomes in the GnomAD database, including 22,694 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 0.54 (22694 hom., cov: 32)
• Consequence: LOC105376360 NR_131187.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.217

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376360	NR_131187.1	n.163-209659A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000654955.1	n.257-1998T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81667 AN: 151926 Hom.: 22686 Cov.: 32

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.537 AC: 81716 AN: 152044 Hom.: 22694 Cov.: 32 AF XY: 0.535 AC XY: 39760 AN XY: 74310

Gnomad4 AFR AF: 0.410

Gnomad4 AMR AF: 0.529

Gnomad4 ASJ AF: 0.673

Gnomad4 EAS AF: 0.368

Gnomad4 SAS AF: 0.592

Gnomad4 FIN AF: 0.545

Gnomad4 NFE AF: 0.618

Gnomad4 OTH AF: 0.557

Alfa AF: 0.579 Hom.: 5771

Bravo AF: 0.527

Asia WGS AF: 0.460 AC: 1599 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.043
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10795055; hg19: chr10-3581221;