rs1003063

Variant names:

• chr6-9487443-G-A
• rs1003063

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 0.0521 in 152,174 control chromosomes in the GnomAD database, including 322 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 0.052 (322 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.211 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: 0.0522 AC: 7933 AN: 152056 Hom.: 324 Cov.: 32

Gnomad AFR AF: 0.0199

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0612

Gnomad ASJ AF: 0.0484

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0597

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0512

Gnomad OTH AF: 0.0570

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

GnomAD4 genome AF: 0.0521 AC: 7924 AN: 152174 Hom.: 322 Cov.: 32 AF XY: 0.0546 AC XY: 4061 AN XY: 74390

African (AFR) AF: 0.0199 AC: 825 AN: 41532

American (AMR) AF: 0.0611 AC: 934 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0484 AC: 168 AN: 3470

East Asian (EAS) AF: 0.221 AC: 1142 AN: 5156

South Asian (SAS) AF: 0.113 AC: 545 AN: 4820

European-Finnish (FIN) AF: 0.0597 AC: 632 AN: 10590

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0512 AC: 3484 AN: 68002

Other (OTH) AF: 0.0564 AC: 119 AN: 2110

Alfa AF: 0.0519 Hom.: 222

Bravo AF: 0.0523

Asia WGS AF: 0.143 AC: 497 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.34
DANN	Benign	0.51
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs1003063; hg19: chr6-9487676;