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. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 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. Variant has been reported in Lovd as Likely benign (no stars).

• Frequency: Genomes: 𝑓 0.30 (7453 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP6: Variant 19-40988986-T-C is Benign according to our data. Variant chr19-40988986-T-C is described in Lovd as [Likely_benign].
• 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

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.360

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.440

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.298

Alfa AF: 0.327 Hom.: 9727

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7254579; hg19: chr19-41494891;