6-6009615-T-G

Variant names:

• chr6-6009615-T-G
• rs3763180

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 0.601 in 152,124 control chromosomes in the GnomAD database, including 28,410 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 0.60 (28410 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.635
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.753 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.601 AC: 91305 AN: 152006 Hom.: 28381 Cov.: 33

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.601 AC: 91380 AN: 152124 Hom.: 28410 Cov.: 33 AF XY: 0.594 AC XY: 44147 AN XY: 74354

African (AFR) AF: 0.760 AC: 31540 AN: 41492

American (AMR) AF: 0.546 AC: 8356 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.620 AC: 2152 AN: 3472

East Asian (EAS) AF: 0.496 AC: 2568 AN: 5176

South Asian (SAS) AF: 0.503 AC: 2424 AN: 4818

European-Finnish (FIN) AF: 0.479 AC: 5067 AN: 10568

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.549 AC: 37308 AN: 67984

Other (OTH) AF: 0.580 AC: 1225 AN: 2112

Alfa AF: 0.563 Hom.: 41384

Bravo AF: 0.614

Asia WGS AF: 0.522 AC: 1816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.64
DANN	Benign	0.49
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs3763180; hg19: chr6-6009848;