chr5-103568046-G-A

Variant names:

• chr5-103568046-G-A
• rs9327886

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 0.527 in 152,020 control chromosomes in the GnomAD database, including 21,511 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 0.53 (21511 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.411

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 = 0.624 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: 0.527 AC: 80085 AN: 151900 Hom.: 21511 Cov.: 32

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.725

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.527 AC: 80109 AN: 152020 Hom.: 21511 Cov.: 32 AF XY: 0.531 AC XY: 39438 AN XY: 74300

African (AFR) AF: 0.427 AC: 17680 AN: 41430

American (AMR) AF: 0.473 AC: 7224 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.540 AC: 1874 AN: 3468

East Asian (EAS) AF: 0.454 AC: 2340 AN: 5150

South Asian (SAS) AF: 0.643 AC: 3098 AN: 4818

European-Finnish (FIN) AF: 0.630 AC: 6658 AN: 10568

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.578 AC: 39320 AN: 67984

Other (OTH) AF: 0.519 AC: 1097 AN: 2114

Alfa AF: 0.555 Hom.: 39292

Bravo AF: 0.508

Asia WGS AF: 0.558 AC: 1938 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	0.31
DANN	Benign	0.56
PhyloP100		-0.41

Splicing

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

Publications

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Other links and lift over

dbSNP: rs9327886; hg19: chr5-102903747;