rs10495997

chr2-51524392-C-G

Variant summary

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

The NR_135237.1(LOC730100):n.695-3210C>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 0.0355 in 152,206 control chromosomes in the GnomAD database, including 233 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 0.036 (233 hom., cov: 32)
• Consequence: LOC730100 NR_135237.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC730100	NR_135237.1	n.695-3210C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000440698.1	n.695-3210C>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0356 AC: 5411 AN: 152088 Hom.: 233 Cov.: 32

Gnomad AFR AF: 0.00720

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0631

Gnomad ASJ AF: 0.0127

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.0687

Gnomad FIN AF: 0.0683

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0286

Gnomad OTH AF: 0.0282

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

GnomAD4 genome AF: 0.0355 AC: 5407 AN: 152206 Hom.: 233 Cov.: 32 AF XY: 0.0399 AC XY: 2971 AN XY: 74432

Gnomad4 AFR AF: 0.00717

Gnomad4 AMR AF: 0.0629

Gnomad4 ASJ AF: 0.0127

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.0682

Gnomad4 FIN AF: 0.0683

Gnomad4 NFE AF: 0.0286

Gnomad4 OTH AF: 0.0284

Alfa AF: 0.0257 Hom.: 8

Bravo AF: 0.0346

Asia WGS AF: 0.121 AC: 418 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.6
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10495997; hg19: chr2-51751530;