chr4-827702-A-G

Variant names:

• chr4-827702-A-G
• rs936551

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 0.525 in 150,504 control chromosomes in the GnomAD database, including 20,921 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 0.52 (20921 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157
• Publications: 11 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 (SAS) allele frequency at 95% confidence interval = 0.587 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: 0.525 AC: 78900 AN: 150388 Hom.: 20899 Cov.: 30

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.574

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.525 AC: 78958 AN: 150504 Hom.: 20921 Cov.: 30 AF XY: 0.521 AC XY: 38251 AN XY: 73434

African (AFR) AF: 0.561 AC: 22939 AN: 40864

American (AMR) AF: 0.449 AC: 6812 AN: 15162

Ashkenazi Jewish (ASJ) AF: 0.588 AC: 2032 AN: 3456

East Asian (EAS) AF: 0.559 AC: 2836 AN: 5076

South Asian (SAS) AF: 0.606 AC: 2863 AN: 4726

European-Finnish (FIN) AF: 0.471 AC: 4883 AN: 10378

Middle Eastern (MID) AF: 0.566 AC: 164 AN: 290

European-Non Finnish (NFE) AF: 0.515 AC: 34814 AN: 67550

Other (OTH) AF: 0.544 AC: 1140 AN: 2094

Alfa AF: 0.520 Hom.: 79847

Bravo AF: 0.523

Asia WGS AF: 0.612 AC: 2128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.6
DANN	Benign	0.41
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs936551; hg19: chr4-821490;