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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376755	XR_007088699.1	n.197-49637C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;