chr6-6012770-C-T

Variant names:

• chr6-6012770-C-T
• rs9405284

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 0.356 in 151,742 control chromosomes in the GnomAD database, including 10,372 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 0.36 (10372 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.903
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.5 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: 0.356 AC: 53920 AN: 151624 Hom.: 10360 Cov.: 31

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.356 AC: 53959 AN: 151742 Hom.: 10372 Cov.: 31 AF XY: 0.352 AC XY: 26131 AN XY: 74174

African (AFR) AF: 0.506 AC: 20839 AN: 41204

American (AMR) AF: 0.313 AC: 4777 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 964 AN: 3468

East Asian (EAS) AF: 0.282 AC: 1459 AN: 5168

South Asian (SAS) AF: 0.331 AC: 1590 AN: 4804

European-Finnish (FIN) AF: 0.289 AC: 3052 AN: 10552

Middle Eastern (MID) AF: 0.223 AC: 65 AN: 292

European-Non Finnish (NFE) AF: 0.296 AC: 20092 AN: 67960

Other (OTH) AF: 0.349 AC: 737 AN: 2114

Alfa AF: 0.317 Hom.: 25139

Bravo AF: 0.362

Asia WGS AF: 0.327 AC: 1135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	12
DANN	Benign	0.83
PhyloP100		0.90

Splicing

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

Other links and lift over

dbSNP: rs9405284; hg19: chr6-6013003;