rs3130171

Variant names:

• chr6-33030952-T-C
• rs3130171

Your query was ambiguous. Multiple possible variants found:

• chr6-33030952-T-C
• chr6-33030952-T-G

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 0.418 in 152,036 control chromosomes in the GnomAD database, including 13,903 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 0.42 (13903 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178
• Publications: 26 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.54 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: 0.418 AC: 63471 AN: 151918 Hom.: 13873 Cov.: 32

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.418 AC: 63533 AN: 152036 Hom.: 13903 Cov.: 32 AF XY: 0.411 AC XY: 30535 AN XY: 74312

African (AFR) AF: 0.546 AC: 22650 AN: 41454

American (AMR) AF: 0.322 AC: 4922 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 777 AN: 3466

East Asian (EAS) AF: 0.417 AC: 2154 AN: 5170

South Asian (SAS) AF: 0.263 AC: 1272 AN: 4828

European-Finnish (FIN) AF: 0.349 AC: 3686 AN: 10548

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.395 AC: 26831 AN: 67968

Other (OTH) AF: 0.411 AC: 869 AN: 2112

Alfa AF: 0.399 Hom.: 43937

Bravo AF: 0.423

Asia WGS AF: 0.316 AC: 1097 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	11
DANN	Benign	0.76
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs3130171; hg19: chr6-32998729;