rs4804765

Variant names:

• chr19-7672954-G-T
• rs4804765

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 0.381 in 151,866 control chromosomes in the GnomAD database, including 12,383 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 0.38 (12383 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.497
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57739 AN: 151748 Hom.: 12364 Cov.: 31

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.0789

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.381 AC: 57797 AN: 151866 Hom.: 12383 Cov.: 31 AF XY: 0.372 AC XY: 27633 AN XY: 74202

African (AFR) AF: 0.579 AC: 23963 AN: 41384

American (AMR) AF: 0.411 AC: 6271 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1073 AN: 3470

East Asian (EAS) AF: 0.0785 AC: 406 AN: 5170

South Asian (SAS) AF: 0.172 AC: 827 AN: 4812

European-Finnish (FIN) AF: 0.247 AC: 2609 AN: 10572

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.317 AC: 21554 AN: 67890

Other (OTH) AF: 0.360 AC: 759 AN: 2108

Alfa AF: 0.348 Hom.: 22304

Bravo AF: 0.400

Asia WGS AF: 0.174 AC: 610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.73
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs4804765; hg19: chr19-7737840;