6-50639223-T-C

Variant names:

• chr6-50639223-T-C
• rs280309

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 0.208 in 152,050 control chromosomes in the GnomAD database, including 5,096 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 0.21 (5096 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.1).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.453 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: 0.208 AC: 31564 AN: 151932 Hom.: 5074 Cov.: 32

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.00732

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0993

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.208 AC: 31625 AN: 152050 Hom.: 5096 Cov.: 32 AF XY: 0.203 AC XY: 15126 AN XY: 74330

African (AFR) AF: 0.459 AC: 18991 AN: 41410

American (AMR) AF: 0.133 AC: 2025 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 621 AN: 3470

East Asian (EAS) AF: 0.00734 AC: 38 AN: 5176

South Asian (SAS) AF: 0.123 AC: 594 AN: 4822

European-Finnish (FIN) AF: 0.0993 AC: 1053 AN: 10600

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.114 AC: 7742 AN: 68002

Other (OTH) AF: 0.183 AC: 387 AN: 2114

Alfa AF: 0.159 Hom.: 1111

Bravo AF: 0.221

Asia WGS AF: 0.0870 AC: 303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.30
DANN	Benign	0.35
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs280309; hg19: chr6-50606936;