6-30856755-C-T

Variant names:

• chr6-30856755-C-T
• rs2844659

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 0.171 in 152,136 control chromosomes in the GnomAD database, including 2,372 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 0.17 (2372 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.553
• Publications: 32 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25900 AN: 152018 Hom.: 2363 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.0715

Gnomad SAS AF: 0.0956

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.171 AC: 25949 AN: 152136 Hom.: 2372 Cov.: 32 AF XY: 0.165 AC XY: 12251 AN XY: 74360

African (AFR) AF: 0.181 AC: 7520 AN: 41484

American (AMR) AF: 0.114 AC: 1747 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 438 AN: 3470

East Asian (EAS) AF: 0.0716 AC: 371 AN: 5180

South Asian (SAS) AF: 0.0965 AC: 466 AN: 4828

European-Finnish (FIN) AF: 0.138 AC: 1465 AN: 10592

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13420 AN: 67980

Other (OTH) AF: 0.134 AC: 283 AN: 2114

Alfa AF: 0.189 Hom.: 6875

Bravo AF: 0.171

Asia WGS AF: 0.0860 AC: 301 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.34
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs2844659; hg19: chr6-30824532;