rs910320

Positions:

• chr6-33107666-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 0.257 in 152,036 control chromosomes in the GnomAD database, including 5,543 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 0.26 (5543 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.128

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 (AFR) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39113 AN: 151918 Hom.: 5536 Cov.: 32

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.0842

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.257 AC: 39137 AN: 152036 Hom.: 5543 Cov.: 32 AF XY: 0.253 AC XY: 18807 AN XY: 74290

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.0842

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.222

Gnomad4 OTH AF: 0.233

Alfa AF: 0.242 Hom.: 931

Bravo AF: 0.257

Asia WGS AF: 0.255 AC: 887 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	5.3
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs910320; hg19: chr6-33075443;