chr2-104542180-A-G

Variant names:

• chr2-104542180-A-G
• rs17624523

Variant summary

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

The variant allele was found at a frequency of 0.21 in 152,090 control chromosomes in the GnomAD database, including 4,089 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 0.21 (4089 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.781

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.347 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: 0.211 AC: 32005 AN: 151974 Hom.: 4091 Cov.: 32

Gnomad AFR AF: 0.0719

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.0680

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.210 AC: 32005 AN: 152090 Hom.: 4089 Cov.: 32 AF XY: 0.212 AC XY: 15773 AN XY: 74344

Gnomad4 AFR AF: 0.0718

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.0681

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.229

Alfa AF: 0.231 Hom.: 816

Bravo AF: 0.198

Asia WGS AF: 0.179 AC: 620 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	6.1
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17624523; hg19: chr2-105158638;