rs10497750

Variant names:

• chr2-195183939-C-A
• rs10497750
• XR_007088699.1:n.196+21039G>T

Your query was ambiguous. Multiple possible variants found:

• chr2-195183939-C-A
• chr2-195183939-C-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.196+21039G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0842 in 152,170 control chromosomes in the GnomAD database, including 710 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 0.084 (710 hom., cov: 32)
• Consequence: LOC105376755 XR_007088699.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720
• Publications: 2 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.15 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: 0.0843 AC: 12813 AN: 152052 Hom.: 713 Cov.: 32

Gnomad AFR AF: 0.0220

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0899

Gnomad EAS AF: 0.0689

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.0987

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

GnomAD4 genome AF: 0.0842 AC: 12812 AN: 152170 Hom.: 710 Cov.: 32 AF XY: 0.0859 AC XY: 6391 AN XY: 74374

African (AFR) AF: 0.0220 AC: 912 AN: 41548

American (AMR) AF: 0.102 AC: 1554 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0899 AC: 312 AN: 3470

East Asian (EAS) AF: 0.0689 AC: 356 AN: 5168

South Asian (SAS) AF: 0.159 AC: 767 AN: 4816

European-Finnish (FIN) AF: 0.118 AC: 1253 AN: 10586

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7226 AN: 68000

Other (OTH) AF: 0.101 AC: 214 AN: 2110

Alfa AF: 0.0686 Hom.: 133

Bravo AF: 0.0785

Asia WGS AF: 0.111 AC: 387 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.63
PhyloP100		0.072

Splicing

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

Other links and lift over

dbSNP: rs10497750; hg19: chr2-196048663;