chr6-60665619-G-C

Variant names:

• chr6-60665619-G-C
• rs6901567

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 0.339 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.339 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

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.419

Gnomad4 ASJ AF: 0.311

Gnomad4 EAS AF: 0.519

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.386

Gnomad4 OTH AF: 0.367

Alfa AF: 0.221 Hom.: 555

Bravo AF: 0.337

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6901567; hg19: chr6-57633366;