rs6859974

Variant names:

• chr5-180778938-C-T
• rs6859974

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 0.351 in 151,362 control chromosomes in the GnomAD database, including 10,994 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 0.35 (10994 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.757
• Publications: 2 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 (AFR) allele frequency at 95% confidence interval = 0.567 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: 0.350 AC: 52993 AN: 151250 Hom.: 10960 Cov.: 31

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.298

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.351 AC: 53078 AN: 151362 Hom.: 10994 Cov.: 31 AF XY: 0.349 AC XY: 25841 AN XY: 73942

African (AFR) AF: 0.573 AC: 23602 AN: 41166

American (AMR) AF: 0.314 AC: 4783 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 906 AN: 3466

East Asian (EAS) AF: 0.342 AC: 1758 AN: 5140

South Asian (SAS) AF: 0.483 AC: 2320 AN: 4804

European-Finnish (FIN) AF: 0.225 AC: 2334 AN: 10390

Middle Eastern (MID) AF: 0.290 AC: 84 AN: 290

European-Non Finnish (NFE) AF: 0.241 AC: 16364 AN: 67860

Other (OTH) AF: 0.329 AC: 690 AN: 2100

Alfa AF: 0.280 Hom.: 5786

Bravo AF: 0.364

Asia WGS AF: 0.435 AC: 1513 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	2.7
DANN	Benign	0.62
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs6859974; hg19: chr5-180205938;