rs6594643

Variant names:

• chr5-112698853-C-A
• rs6594643

Your query was ambiguous. Multiple possible variants found:

• chr5-112698853-C-A
• chr5-112698853-C-G

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 0.579 in 152,018 control chromosomes in the GnomAD database, including 25,868 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 0.58 (25868 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.765 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: 0.579 AC: 87931 AN: 151896 Hom.: 25839 Cov.: 32

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.539

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.579 AC: 88016 AN: 152018 Hom.: 25868 Cov.: 32 AF XY: 0.581 AC XY: 43133 AN XY: 74298

African (AFR) AF: 0.599 AC: 24817 AN: 41446

American (AMR) AF: 0.644 AC: 9853 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1837 AN: 3470

East Asian (EAS) AF: 0.785 AC: 4058 AN: 5170

South Asian (SAS) AF: 0.641 AC: 3087 AN: 4816

European-Finnish (FIN) AF: 0.492 AC: 5190 AN: 10558

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.549 AC: 37294 AN: 67958

Other (OTH) AF: 0.586 AC: 1236 AN: 2110

Alfa AF: 0.550 Hom.: 2916

Bravo AF: 0.595

Asia WGS AF: 0.712 AC: 2474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.64
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs6594643; hg19: chr5-112034550;