rs1565924

Variant names:

• chr4-11509828-G-A
• rs1565924

Your query was ambiguous. Multiple possible variants found:

• chr4-11509828-G-A
• chr4-11509828-G-C

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 0.611 in 151,818 control chromosomes in the GnomAD database, including 29,013 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 0.61 (29013 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.388
• Publications: 6 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 = 0.786 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: 0.611 AC: 92662 AN: 151698 Hom.: 28990 Cov.: 30

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.675

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.611 AC: 92723 AN: 151818 Hom.: 29013 Cov.: 30 AF XY: 0.610 AC XY: 45259 AN XY: 74208

African (AFR) AF: 0.465 AC: 19259 AN: 41382

American (AMR) AF: 0.576 AC: 8764 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.596 AC: 2067 AN: 3468

East Asian (EAS) AF: 0.806 AC: 4142 AN: 5136

South Asian (SAS) AF: 0.657 AC: 3157 AN: 4808

European-Finnish (FIN) AF: 0.640 AC: 6742 AN: 10540

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.684 AC: 46459 AN: 67946

Other (OTH) AF: 0.648 AC: 1368 AN: 2110

Alfa AF: 0.657 Hom.: 57021

Bravo AF: 0.602

Asia WGS AF: 0.708 AC: 2460 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.26
DANN	Benign	0.67
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs1565924; hg19: chr4-11511452;