rs172274

Positions:

• chr6-33001680-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.372 in 152,182 control chromosomes in the GnomAD database, including 10,915 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 0.37 (10915 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56592 AN: 152064 Hom.: 10912 Cov.: 33

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.372 AC: 56644 AN: 152182 Hom.: 10915 Cov.: 33 AF XY: 0.372 AC XY: 27671 AN XY: 74426

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.497

Gnomad4 ASJ AF: 0.537

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.466

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.349

Gnomad4 OTH AF: 0.423

Alfa AF: 0.363 Hom.: 13306

Bravo AF: 0.392

Asia WGS AF: 0.424 AC: 1474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.1
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs172274; hg19: chr6-32969457;