6-33011902-G-C

Variant names:

• chr6-33011902-G-C
• rs432375

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 0.108 in 152,232 control chromosomes in the GnomAD database, including 1,150 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 0.11 (1150 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.330
• Publications: 5 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 (AFR) allele frequency at 95% confidence interval = 0.19 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: 0.108 AC: 16413 AN: 152114 Hom.: 1147 Cov.: 33

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0975

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.0441

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0125

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.0753

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.108 AC: 16447 AN: 152232 Hom.: 1150 Cov.: 33 AF XY: 0.103 AC XY: 7692 AN XY: 74448

African (AFR) AF: 0.194 AC: 8052 AN: 41520

American (AMR) AF: 0.0973 AC: 1488 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 470 AN: 3468

East Asian (EAS) AF: 0.0442 AC: 229 AN: 5182

South Asian (SAS) AF: 0.122 AC: 587 AN: 4826

European-Finnish (FIN) AF: 0.0125 AC: 133 AN: 10622

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.0753 AC: 5119 AN: 68010

Other (OTH) AF: 0.134 AC: 282 AN: 2112

Alfa AF: 0.0935 Hom.: 100

Bravo AF: 0.119

Asia WGS AF: 0.0940 AC: 329 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	1.8
DANN	Benign	0.71
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs432375; hg19: chr6-32979679;