6-50853227-T-C

Variant names:

• chr6-50853227-T-C
• rs2635727

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 0.743 in 152,076 control chromosomes in the GnomAD database, including 41,952 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 0.74 (41952 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.778 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: 0.743 AC: 112863 AN: 151956 Hom.: 41915 Cov.: 32

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.798

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.720

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

GnomAD4 genome AF: 0.743 AC: 112955 AN: 152076 Hom.: 41952 Cov.: 32 AF XY: 0.740 AC XY: 55051 AN XY: 74348

Gnomad4 AFR AF: 0.729

Gnomad4 AMR AF: 0.765

Gnomad4 ASJ AF: 0.657

Gnomad4 EAS AF: 0.798

Gnomad4 SAS AF: 0.707

Gnomad4 FIN AF: 0.728

Gnomad4 NFE AF: 0.752

Gnomad4 OTH AF: 0.723

Alfa AF: 0.742 Hom.: 82072

Bravo AF: 0.745

Asia WGS AF: 0.775 AC: 2693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.48
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2635727; hg19: chr6-50820940;