rs7255904

Variant names:

• chr19-41023115-G-A
• rs7255904

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 0.491 in 151,846 control chromosomes in the GnomAD database, including 18,864 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 0.49 (18864 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.319
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.635 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: 0.492 AC: 74581 AN: 151728 Hom.: 18856 Cov.: 31

Gnomad AFR AF: 0.536

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.491 AC: 74627 AN: 151846 Hom.: 18864 Cov.: 31 AF XY: 0.495 AC XY: 36749 AN XY: 74190

African (AFR) AF: 0.536 AC: 22186 AN: 41388

American (AMR) AF: 0.646 AC: 9853 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.590 AC: 2045 AN: 3468

East Asian (EAS) AF: 0.390 AC: 2006 AN: 5138

South Asian (SAS) AF: 0.593 AC: 2850 AN: 4808

European-Finnish (FIN) AF: 0.425 AC: 4484 AN: 10546

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29547 AN: 67930

Other (OTH) AF: 0.522 AC: 1101 AN: 2108

Alfa AF: 0.494 Hom.: 3111

Bravo AF: 0.506

Asia WGS AF: 0.505 AC: 1752 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.082
DANN	Benign	0.63
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs7255904; hg19: chr19-41529020;