6-92962125-G-C

Variant names:

• chr6-92962125-G-C
• rs2485846

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 0.204 in 151,904 control chromosomes in the GnomAD database, including 5,714 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 0.20 (5714 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.53
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.738 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: 0.204 AC: 30980 AN: 151786 Hom.: 5712 Cov.: 32

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.0626

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.0544

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.0586

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.204 AC: 31019 AN: 151904 Hom.: 5714 Cov.: 32 AF XY: 0.209 AC XY: 15550 AN XY: 74230

African (AFR) AF: 0.399 AC: 16525 AN: 41418

American (AMR) AF: 0.248 AC: 3781 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 560 AN: 3470

East Asian (EAS) AF: 0.758 AC: 3901 AN: 5148

South Asian (SAS) AF: 0.241 AC: 1157 AN: 4800

European-Finnish (FIN) AF: 0.0544 AC: 575 AN: 10574

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.0586 AC: 3985 AN: 67952

Other (OTH) AF: 0.202 AC: 426 AN: 2112

Alfa AF: 0.0495 Hom.: 69

Bravo AF: 0.231

Asia WGS AF: 0.470 AC: 1629 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.032
DANN	Benign	0.40
PhyloP100		-3.5

Splicing

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

Other links and lift over

dbSNP: rs2485846; hg19: chr6-93671843;