rs1566485

Variant names:

• chr4-77621443-A-C
• rs1566485

Your query was ambiguous. Multiple possible variants found:

• chr4-77621443-A-C
• chr4-77621443-A-G
• chr4-77621443-A-T

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 0.504 in 151,018 control chromosomes in the GnomAD database, including 20,609 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 0.50 (20609 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.679
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.702 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: 0.504 AC: 76109 AN: 150898 Hom.: 20610 Cov.: 29

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.504 AC: 76126 AN: 151018 Hom.: 20609 Cov.: 29 AF XY: 0.509 AC XY: 37549 AN XY: 73716

African (AFR) AF: 0.288 AC: 11780 AN: 40930

American (AMR) AF: 0.591 AC: 8997 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1802 AN: 3466

East Asian (EAS) AF: 0.722 AC: 3700 AN: 5128

South Asian (SAS) AF: 0.537 AC: 2563 AN: 4776

European-Finnish (FIN) AF: 0.656 AC: 6831 AN: 10408

Middle Eastern (MID) AF: 0.490 AC: 143 AN: 292

European-Non Finnish (NFE) AF: 0.571 AC: 38701 AN: 67782

Other (OTH) AF: 0.506 AC: 1064 AN: 2104

Alfa AF: 0.546 Hom.: 87406

Bravo AF: 0.490

Asia WGS AF: 0.581 AC: 2021 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.45
DANN	Benign	0.80
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs1566485; hg19: chr4-78542597;