rs6594644

Variant names:

• chr5-112698899-T-G
• rs6594644

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 0.582 in 152,070 control chromosomes in the GnomAD database, including 26,207 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 (26207 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.794 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: 0.582 AC: 88435 AN: 151950 Hom.: 26183 Cov.: 33

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.815

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.582 AC: 88514 AN: 152070 Hom.: 26207 Cov.: 33 AF XY: 0.584 AC XY: 43376 AN XY: 74332

African (AFR) AF: 0.599 AC: 24834 AN: 41434

American (AMR) AF: 0.647 AC: 9897 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1839 AN: 3466

East Asian (EAS) AF: 0.814 AC: 4214 AN: 5174

South Asian (SAS) AF: 0.643 AC: 3099 AN: 4820

European-Finnish (FIN) AF: 0.492 AC: 5211 AN: 10590

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

European-Non Finnish (NFE) AF: 0.552 AC: 37526 AN: 67982

Other (OTH) AF: 0.590 AC: 1248 AN: 2114

Alfa AF: 0.553 Hom.: 2948

Bravo AF: 0.598

Asia WGS AF: 0.725 AC: 2518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.7
DANN	Benign	0.74
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs6594644; hg19: chr5-112034596;