chr2-72167620-A-G

Variant names:

• chr2-72167620-A-G
• rs194243

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 0.358 in 152,020 control chromosomes in the GnomAD database, including 10,948 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 0.36 (10948 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.574
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.524 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: 0.358 AC: 54350 AN: 151902 Hom.: 10919 Cov.: 32

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.0287

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.358 AC: 54428 AN: 152020 Hom.: 10948 Cov.: 32 AF XY: 0.350 AC XY: 26038 AN XY: 74332

African (AFR) AF: 0.530 AC: 21951 AN: 41450

American (AMR) AF: 0.301 AC: 4598 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 798 AN: 3460

East Asian (EAS) AF: 0.0288 AC: 149 AN: 5172

South Asian (SAS) AF: 0.152 AC: 733 AN: 4814

European-Finnish (FIN) AF: 0.314 AC: 3327 AN: 10586

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.321 AC: 21842 AN: 67976

Other (OTH) AF: 0.332 AC: 698 AN: 2104

Alfa AF: 0.328 Hom.: 2735

Bravo AF: 0.365

Asia WGS AF: 0.129 AC: 448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.5
DANN	Benign	0.81
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs194243; hg19: chr2-72394749;