rs6859974

chr5-180778938-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.573

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.342

Gnomad4 SAS AF: 0.483

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.329

Alfa AF: 0.243 Hom.: 2113

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6859974; hg19: chr5-180205938;