chr2-223970652-C-T

Variant names:

• chr2-223970652-C-T
• rs1025734

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 0.356 in 152,116 control chromosomes in the GnomAD database, including 11,371 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 0.36 (11371 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.853
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.479 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: 0.356 AC: 54107 AN: 151998 Hom.: 11370 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.356 AC: 54102 AN: 152116 Hom.: 11371 Cov.: 32 AF XY: 0.362 AC XY: 26882 AN XY: 74358

African (AFR) AF: 0.123 AC: 5089 AN: 41510

American (AMR) AF: 0.396 AC: 6055 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1127 AN: 3468

East Asian (EAS) AF: 0.281 AC: 1456 AN: 5182

South Asian (SAS) AF: 0.495 AC: 2385 AN: 4816

European-Finnish (FIN) AF: 0.505 AC: 5344 AN: 10574

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.463 AC: 31449 AN: 67972

Other (OTH) AF: 0.345 AC: 727 AN: 2110

Alfa AF: 0.423 Hom.: 16959

Bravo AF: 0.334

Asia WGS AF: 0.340 AC: 1186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.8
DANN	Benign	0.82
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs1025734; hg19: chr2-224835369;