rs10497151

Positions:

• chr2-155840584-A-G

Variant summary

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

The XR_007088689.1(LOC105373703):​n.635-26440T>C 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 0.0669 in 152,074 control chromosomes in the GnomAD database, including 425 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 0.067 (425 hom., cov: 32)
• Consequence: LOC105373703 XR_007088689.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.33

Genes affected

LOC105373703 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0833 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373703	XR_007088689.1	n.635-26440T>C		intron_variant, non_coding_transcript_variant
LOC105373703	XR_001739749.2	n.1019+19T>C		intron_variant, non_coding_transcript_variant
LOC105373703	XR_001739750.2	n.1019+19T>C		intron_variant, non_coding_transcript_variant
LOC105373703	XR_001739751.2	n.1019+19T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0670 AC: 10180 AN: 151956 Hom.: 426 Cov.: 32

Gnomad AFR AF: 0.0547

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.0459

Gnomad ASJ AF: 0.0855

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0128

Gnomad FIN AF: 0.0785

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0851

Gnomad OTH AF: 0.0647

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

GnomAD4 genome AF: 0.0669 AC: 10178 AN: 152074 Hom.: 425 Cov.: 32 AF XY: 0.0654 AC XY: 4863 AN XY: 74366

Gnomad4 AFR AF: 0.0545

Gnomad4 AMR AF: 0.0457

Gnomad4 ASJ AF: 0.0855

Gnomad4 EAS AF: 0.000773

Gnomad4 SAS AF: 0.0128

Gnomad4 FIN AF: 0.0785

Gnomad4 NFE AF: 0.0851

Gnomad4 OTH AF: 0.0640

Alfa AF: 0.0777 Hom.: 219

Bravo AF: 0.0644

Asia WGS AF: 0.0160 AC: 56 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	13
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10497151; hg19: chr2-156697096;