rs10497748

Variant names:

• chr2-195109140-G-A
• rs10497748
• XR_007088699.1:n.197-49637C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007088699.1(LOC105376755):​n.197-49637C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0296 in 152,136 control chromosomes in the GnomAD database, including 119 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 0.030 (119 hom., cov: 32)
• Consequence: LOC105376755 XR_007088699.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14
• Publications: 1 publications found

Genes affected

LOC105376755 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.065 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0295 AC: 4488 AN: 152018 Hom.: 116 Cov.: 32

Gnomad AFR AF: 0.0160

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0337

Gnomad ASJ AF: 0.0228

Gnomad EAS AF: 0.0566

Gnomad SAS AF: 0.0714

Gnomad FIN AF: 0.0936

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0227

Gnomad OTH AF: 0.0259

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

GnomAD4 genome AF: 0.0296 AC: 4509 AN: 152136 Hom.: 119 Cov.: 32 AF XY: 0.0334 AC XY: 2483 AN XY: 74378

African (AFR) AF: 0.0164 AC: 681 AN: 41526

American (AMR) AF: 0.0336 AC: 513 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0228 AC: 79 AN: 3466

East Asian (EAS) AF: 0.0563 AC: 291 AN: 5168

South Asian (SAS) AF: 0.0712 AC: 343 AN: 4816

European-Finnish (FIN) AF: 0.0936 AC: 992 AN: 10602

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0227 AC: 1544 AN: 67982

Other (OTH) AF: 0.0285 AC: 60 AN: 2108

Alfa AF: 0.0268 Hom.: 44

Bravo AF: 0.0230

Asia WGS AF: 0.0690 AC: 240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	14
DANN	Benign	0.80
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs10497748; hg19: chr2-195973864;