rs10201742

Positions:

• chr2-126571196-A-C
• chr2-126571196-A-G

Variant summary

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

The XR_001739693.1(LOC105373602):​n.211-34679T>G 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 0.263 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

Genes affected

LOC105373602 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373602	XR_001739693.1	n.211-34679T>G		intron_variant, non_coding_transcript_variant

Ensembl

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

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

Gnomad4 AFR AF: 0.509

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.0276

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.218

Alfa AF: 0.172 Hom.: 1131

Bravo AF: 0.273

Asia WGS AF: 0.0960 AC: 334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10201742; hg19: chr2-127328773;