rs2486758

Variant names:

• chr10-102837723-T-C
• rs2486758

Your query was ambiguous. Multiple possible variants found:

• chr10-102837723-T-C
• chr10-102837723-T-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.184 in 152,064 control chromosomes in the GnomAD database, including 3,114 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.18 (3114 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.855

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BP6: Variant 10-102837723-T-C is Benign according to our data. Variant chr10-102837723-T-C is described in ClinVar as [Benign]. Clinvar id is 1247676.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.184 AC: 27970 AN: 151948 Hom.: 3107 Cov.: 31

Gnomad AFR AF: 0.0682

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.184 AC: 27983 AN: 152064 Hom.: 3114 Cov.: 31 AF XY: 0.193 AC XY: 14345 AN XY: 74318

Gnomad4 AFR AF: 0.0681

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.189

Alfa AF: 0.211 Hom.: 4922

Bravo AF: 0.174

Asia WGS AF: 0.264 AC: 918 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jun 26, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	3.8
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2486758; hg19: chr10-104597480;