2-126571196-A-C

Variant names:

• chr2-126571196-A-C
• rs10201742
• XR_001739693.1:n.211-34679T>G

Variant summary

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

The XR_001739693.1(LOC105373602):​n.211-34679T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 152,192 control chromosomes in the GnomAD database, including 7,113 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 0.26 (7113 hom., cov: 33)
• Consequence: LOC105373602 XR_001739693.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 2 publications found

Genes affected

LOC105373602 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.503 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: 0.262 AC: 39901 AN: 152074 Hom.: 7082 Cov.: 33

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.0275

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.263 AC: 39986 AN: 152192 Hom.: 7113 Cov.: 33 AF XY: 0.258 AC XY: 19180 AN XY: 74426

African (AFR) AF: 0.509 AC: 21113 AN: 41486

American (AMR) AF: 0.154 AC: 2360 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 484 AN: 3472

East Asian (EAS) AF: 0.0276 AC: 143 AN: 5184

South Asian (SAS) AF: 0.105 AC: 505 AN: 4830

European-Finnish (FIN) AF: 0.175 AC: 1852 AN: 10598

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12885 AN: 68004

Other (OTH) AF: 0.218 AC: 461 AN: 2110

Alfa AF: 0.174 Hom.: 1279

Bravo AF: 0.273

Asia WGS AF: 0.0960 AC: 334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.41
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10201742; hg19: chr2-127328773;