rs7265042

Variant names:

• chr20-55782353-T-C
• rs7265042

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 0.259 in 152,068 control chromosomes in the GnomAD database, including 5,412 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 0.26 (5412 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.499
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.289 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: 0.259 AC: 39318 AN: 151950 Hom.: 5403 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.0434

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.259 AC: 39358 AN: 152068 Hom.: 5412 Cov.: 32 AF XY: 0.254 AC XY: 18885 AN XY: 74350

African (AFR) AF: 0.241 AC: 10006 AN: 41470

American (AMR) AF: 0.213 AC: 3257 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1128 AN: 3470

East Asian (EAS) AF: 0.0433 AC: 224 AN: 5176

South Asian (SAS) AF: 0.215 AC: 1038 AN: 4818

European-Finnish (FIN) AF: 0.276 AC: 2918 AN: 10562

Middle Eastern (MID) AF: 0.418 AC: 122 AN: 292

European-Non Finnish (NFE) AF: 0.293 AC: 19892 AN: 67974

Other (OTH) AF: 0.275 AC: 581 AN: 2112

Alfa AF: 0.285 Hom.: 10529

Bravo AF: 0.253

Asia WGS AF: 0.176 AC: 610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.7
DANN	Benign	0.55
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs7265042; hg19: chr20-54357409;