6-6009615-T-G

Position:

• chr6-6009615-T-G

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 0.601 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.760

Gnomad4 AMR AF: 0.546

Gnomad4 ASJ AF: 0.620

Gnomad4 EAS AF: 0.496

Gnomad4 SAS AF: 0.503

Gnomad4 FIN AF: 0.479

Gnomad4 NFE AF: 0.549

Gnomad4 OTH AF: 0.580

Alfa AF: 0.559 Hom.: 32286

Bravo AF: 0.614

Asia WGS AF: 0.522 AC: 1816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3763180; hg19: chr6-6009848;