rs2270447

Variant names:

• chr2-162103238-T-C
• rs2270447

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 0.117 in 152,076 control chromosomes in the GnomAD database, including 1,465 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 0.12 (1465 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.356 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: 0.117 AC: 17767 AN: 151960 Hom.: 1458 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.0836

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0599

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.117 AC: 17789 AN: 152076 Hom.: 1465 Cov.: 32 AF XY: 0.122 AC XY: 9106 AN XY: 74344

African (AFR) AF: 0.166 AC: 6900 AN: 41456

American (AMR) AF: 0.127 AC: 1943 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 420 AN: 3466

East Asian (EAS) AF: 0.370 AC: 1907 AN: 5152

South Asian (SAS) AF: 0.257 AC: 1236 AN: 4816

European-Finnish (FIN) AF: 0.0836 AC: 885 AN: 10592

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0599 AC: 4074 AN: 68004

Other (OTH) AF: 0.114 AC: 242 AN: 2114

Alfa AF: 0.0839 Hom.: 2285

Bravo AF: 0.122

Asia WGS AF: 0.301 AC: 1048 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.10
DANN	Benign	0.29
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2270447; hg19: chr2-162959748;