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. The variant received -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
• Publications: 43 publications found

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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

African (AFR) AF: 0.0681 AC: 2824 AN: 41490

American (AMR) AF: 0.256 AC: 3913 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 574 AN: 3468

East Asian (EAS) AF: 0.205 AC: 1061 AN: 5168

South Asian (SAS) AF: 0.258 AC: 1244 AN: 4826

European-Finnish (FIN) AF: 0.340 AC: 3585 AN: 10544

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14171 AN: 67984

Other (OTH) AF: 0.189 AC: 398 AN: 2110

Alfa AF: 0.200 Hom.: 6043

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
PhyloP100		-0.85
PromoterAI		-0.12	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2486758; hg19: chr10-104597480;