rs6574859

Variant names:

• chr14-85892223-A-C
• rs6574859

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 0.45 in 152,032 control chromosomes in the GnomAD database, including 18,971 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 0.45 (18971 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.631 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: 0.450 AC: 68358 AN: 151914 Hom.: 18976 Cov.: 31

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.450 AC: 68357 AN: 152032 Hom.: 18971 Cov.: 31 AF XY: 0.443 AC XY: 32924 AN XY: 74278

African (AFR) AF: 0.158 AC: 6568 AN: 41504

American (AMR) AF: 0.411 AC: 6277 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1700 AN: 3472

East Asian (EAS) AF: 0.125 AC: 641 AN: 5142

South Asian (SAS) AF: 0.318 AC: 1525 AN: 4802

European-Finnish (FIN) AF: 0.614 AC: 6491 AN: 10564

Middle Eastern (MID) AF: 0.599 AC: 175 AN: 292

European-Non Finnish (NFE) AF: 0.636 AC: 43263 AN: 67972

Other (OTH) AF: 0.476 AC: 1005 AN: 2112

Alfa AF: 0.563 Hom.: 48618

Bravo AF: 0.422

Asia WGS AF: 0.200 AC: 695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	13
DANN	Benign	0.61
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs6574859; hg19: chr14-86358567; COSMIC: COSV53417124;