6-33000499-G-A

Variant names:

• chr6-33000499-G-A
• rs2395300

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 0.321 in 152,064 control chromosomes in the GnomAD database, including 8,352 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 0.32 (8352 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.648
• Publications: 25 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.44 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: 0.321 AC: 48721 AN: 151946 Hom.: 8352 Cov.: 31

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.321 AC: 48760 AN: 152064 Hom.: 8352 Cov.: 31 AF XY: 0.322 AC XY: 23899 AN XY: 74324

African (AFR) AF: 0.244 AC: 10102 AN: 41476

American (AMR) AF: 0.449 AC: 6867 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1741 AN: 3468

East Asian (EAS) AF: 0.324 AC: 1677 AN: 5170

South Asian (SAS) AF: 0.444 AC: 2134 AN: 4802

European-Finnish (FIN) AF: 0.245 AC: 2588 AN: 10570

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.332 AC: 22561 AN: 67972

Other (OTH) AF: 0.365 AC: 772 AN: 2114

Alfa AF: 0.338 Hom.: 34855

Bravo AF: 0.334

Asia WGS AF: 0.404 AC: 1404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.37
DANN	Benign	0.41
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs2395300; hg19: chr6-32968276;