6-33499957-T-C

Variant names:

• chr6-33499957-T-C
• rs9380362

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 0.589 in 152,040 control chromosomes in the GnomAD database, including 28,304 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 0.59 (28304 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.923 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: 0.589 AC: 89555 AN: 151922 Hom.: 28298 Cov.: 31

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.617

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.945

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.589 AC: 89602 AN: 152040 Hom.: 28304 Cov.: 31 AF XY: 0.603 AC XY: 44798 AN XY: 74328

African (AFR) AF: 0.364 AC: 15088 AN: 41444

American (AMR) AF: 0.646 AC: 9865 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 2206 AN: 3470

East Asian (EAS) AF: 0.945 AC: 4897 AN: 5184

South Asian (SAS) AF: 0.829 AC: 3995 AN: 4820

European-Finnish (FIN) AF: 0.758 AC: 8005 AN: 10564

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.640 AC: 43503 AN: 67972

Other (OTH) AF: 0.616 AC: 1303 AN: 2116

Alfa AF: 0.612 Hom.: 3684

Bravo AF: 0.565

Asia WGS AF: 0.829 AC: 2880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.53
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs9380362; hg19: chr6-33467734;