6-60665619-G-C

Variant names:

• chr6-60665619-G-C
• rs6901567

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 0.339 in 151,546 control chromosomes in the GnomAD database, including 9,439 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 0.34 (9439 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51301 AN: 151432 Hom.: 9432 Cov.: 30

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.339 AC: 51321 AN: 151546 Hom.: 9439 Cov.: 30 AF XY: 0.339 AC XY: 25125 AN XY: 74032

African (AFR) AF: 0.196 AC: 8101 AN: 41240

American (AMR) AF: 0.419 AC: 6380 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1080 AN: 3468

East Asian (EAS) AF: 0.519 AC: 2660 AN: 5122

South Asian (SAS) AF: 0.346 AC: 1663 AN: 4812

European-Finnish (FIN) AF: 0.374 AC: 3911 AN: 10464

Middle Eastern (MID) AF: 0.432 AC: 126 AN: 292

European-Non Finnish (NFE) AF: 0.386 AC: 26235 AN: 67904

Other (OTH) AF: 0.367 AC: 768 AN: 2094

Alfa AF: 0.221 Hom.: 555

Bravo AF: 0.337

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.30
DANN	Benign	0.37
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs6901567; hg19: chr6-57633366;