rs6899062

Variant names:

• chr5-25610654-A-C
• rs6899062

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 0.131 in 152,104 control chromosomes in the GnomAD database, including 1,482 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 0.13 (1482 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.606
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.197 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: 0.131 AC: 19964 AN: 151986 Hom.: 1476 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.0850

Gnomad EAS AF: 0.0483

Gnomad SAS AF: 0.0694

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.131 AC: 19987 AN: 152104 Hom.: 1482 Cov.: 32 AF XY: 0.132 AC XY: 9849 AN XY: 74338

African (AFR) AF: 0.150 AC: 6223 AN: 41490

American (AMR) AF: 0.203 AC: 3103 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0850 AC: 295 AN: 3472

East Asian (EAS) AF: 0.0484 AC: 250 AN: 5160

South Asian (SAS) AF: 0.0690 AC: 333 AN: 4824

European-Finnish (FIN) AF: 0.160 AC: 1699 AN: 10592

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7695 AN: 67968

Other (OTH) AF: 0.116 AC: 244 AN: 2112

Alfa AF: 0.117 Hom.: 592

Bravo AF: 0.134

Asia WGS AF: 0.0730 AC: 254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.63
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs6899062; hg19: chr5-25610763;