2-227933798-C-T

Variant names:

• chr2-227933798-C-T
• rs1403970

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 0.595 in 152,052 control chromosomes in the GnomAD database, including 27,371 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 0.60 (27371 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.682 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: 0.595 AC: 90434 AN: 151932 Hom.: 27374 Cov.: 32

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.567

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.595 AC: 90478 AN: 152052 Hom.: 27371 Cov.: 32 AF XY: 0.595 AC XY: 44199 AN XY: 74322

African (AFR) AF: 0.480 AC: 19920 AN: 41464

American (AMR) AF: 0.693 AC: 10591 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.664 AC: 2305 AN: 3470

East Asian (EAS) AF: 0.567 AC: 2927 AN: 5158

South Asian (SAS) AF: 0.683 AC: 3287 AN: 4814

European-Finnish (FIN) AF: 0.597 AC: 6314 AN: 10568

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.635 AC: 43153 AN: 67972

Other (OTH) AF: 0.624 AC: 1318 AN: 2112

Alfa AF: 0.625 Hom.: 110172

Bravo AF: 0.595

Asia WGS AF: 0.592 AC: 2059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.27
DANN	Benign	0.85
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1403970; hg19: chr2-228798514;