6-33158081-A-C

Variant names:

• chr6-33158081-A-C
• rs3130161

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 0.154 in 151,812 control chromosomes in the GnomAD database, including 2,079 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 0.15 (2079 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0520
• Publications: 22 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 (AFR) allele frequency at 95% confidence interval = 0.23 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: 0.154 AC: 23352 AN: 151692 Hom.: 2069 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0807

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.154 AC: 23395 AN: 151812 Hom.: 2079 Cov.: 32 AF XY: 0.154 AC XY: 11418 AN XY: 74182

African (AFR) AF: 0.234 AC: 9666 AN: 41334

American (AMR) AF: 0.103 AC: 1575 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0807 AC: 280 AN: 3468

East Asian (EAS) AF: 0.126 AC: 650 AN: 5158

South Asian (SAS) AF: 0.159 AC: 763 AN: 4806

European-Finnish (FIN) AF: 0.149 AC: 1566 AN: 10538

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8551 AN: 67916

Other (OTH) AF: 0.133 AC: 280 AN: 2112

Alfa AF: 0.134 Hom.: 3787

Bravo AF: 0.154

Asia WGS AF: 0.171 AC: 593 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	3.5
DANN	Benign	0.43
PhyloP100		0.052

Splicing

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

Other links and lift over

dbSNP: rs3130161; hg19: chr6-33125858;