rs7254579

Variant names:

• chr19-40988986-T-C
• rs7254579

Your query was ambiguous. Multiple possible variants found:

• chr19-40988986-T-C
• chr19-40988986-T-G

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 0.297 in 151,890 control chromosomes in the GnomAD database, including 7,453 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 0.30 (7453 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.425 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: 0.297 AC: 45122 AN: 151772 Hom.: 7453 Cov.: 31

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.297 AC: 45146 AN: 151890 Hom.: 7453 Cov.: 31 AF XY: 0.302 AC XY: 22382 AN XY: 74218

African (AFR) AF: 0.160 AC: 6635 AN: 41394

American (AMR) AF: 0.360 AC: 5486 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1119 AN: 3470

East Asian (EAS) AF: 0.440 AC: 2265 AN: 5152

South Asian (SAS) AF: 0.348 AC: 1672 AN: 4810

European-Finnish (FIN) AF: 0.396 AC: 4179 AN: 10546

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.335 AC: 22786 AN: 67956

Other (OTH) AF: 0.298 AC: 629 AN: 2108

Alfa AF: 0.325 Hom.: 22805

Bravo AF: 0.291

Asia WGS AF: 0.358 AC: 1247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.0
DANN	Benign	0.42
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs7254579; hg19: chr19-41494891;