2-100807315-C-T

Variant names:

• chr2-100807315-C-T
• rs17024792

Variant summary

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

The variant allele was found at a frequency of 0.147 in 152,214 control chromosomes in the GnomAD database, including 2,627 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 0.15 (2627 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0810
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.402 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: 0.147 AC: 22336 AN: 152094 Hom.: 2614 Cov.: 32

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.0670

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.0710

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0592

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.147 AC: 22377 AN: 152214 Hom.: 2627 Cov.: 32 AF XY: 0.148 AC XY: 10991 AN XY: 74428

African (AFR) AF: 0.289 AC: 12006 AN: 41514

American (AMR) AF: 0.124 AC: 1891 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 393 AN: 3468

East Asian (EAS) AF: 0.417 AC: 2149 AN: 5154

South Asian (SAS) AF: 0.149 AC: 717 AN: 4828

European-Finnish (FIN) AF: 0.0710 AC: 754 AN: 10620

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0593 AC: 4031 AN: 68026

Other (OTH) AF: 0.160 AC: 337 AN: 2110

Alfa AF: 0.0942 Hom.: 4002

Bravo AF: 0.160

Asia WGS AF: 0.298 AC: 1036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.4
DANN	Benign	0.76
PhyloP100		0.081

Splicing

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

Other links and lift over

dbSNP: rs17024792; hg19: chr2-101423777;