rs1895699

Variant names:

• chr2-53268066-C-T
• rs1895699

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 0.194 in 152,048 control chromosomes in the GnomAD database, including 3,390 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 0.19 (3390 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.642
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.281 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: 0.194 AC: 29499 AN: 151930 Hom.: 3385 Cov.: 32

Gnomad AFR AF: 0.0718

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.194 AC: 29513 AN: 152048 Hom.: 3390 Cov.: 32 AF XY: 0.194 AC XY: 14394 AN XY: 74300

African (AFR) AF: 0.0717 AC: 2971 AN: 41430

American (AMR) AF: 0.288 AC: 4401 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 886 AN: 3468

East Asian (EAS) AF: 0.228 AC: 1172 AN: 5144

South Asian (SAS) AF: 0.220 AC: 1061 AN: 4820

European-Finnish (FIN) AF: 0.181 AC: 1918 AN: 10580

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16333 AN: 67992

Other (OTH) AF: 0.197 AC: 416 AN: 2112

Alfa AF: 0.216 Hom.: 5807

Bravo AF: 0.195

Asia WGS AF: 0.213 AC: 740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	1.2
DANN	Benign	0.56
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs1895699; hg19: chr2-53495204;