2-55781769-T-C

Variant names:

• chr2-55781769-T-C
• rs7577894

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 0.528 in 152,066 control chromosomes in the GnomAD database, including 23,145 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 0.53 (23145 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.858 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: 0.528 AC: 80205 AN: 151948 Hom.: 23116 Cov.: 32

Gnomad AFR AF: 0.731

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.597

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.528 AC: 80286 AN: 152066 Hom.: 23145 Cov.: 32 AF XY: 0.528 AC XY: 39255 AN XY: 74308

African (AFR) AF: 0.730 AC: 30284 AN: 41460

American (AMR) AF: 0.412 AC: 6303 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1983 AN: 3472

East Asian (EAS) AF: 0.880 AC: 4558 AN: 5182

South Asian (SAS) AF: 0.597 AC: 2881 AN: 4826

European-Finnish (FIN) AF: 0.365 AC: 3851 AN: 10554

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.421 AC: 28605 AN: 67970

Other (OTH) AF: 0.519 AC: 1098 AN: 2116

Alfa AF: 0.465 Hom.: 61414

Bravo AF: 0.539

Asia WGS AF: 0.707 AC: 2461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.6
DANN	Benign	0.71
PhyloP100		-0.0020

Splicing

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

Other links and lift over

dbSNP: rs7577894; hg19: chr2-56008904;