6-45779785-G-A

Position:

• chr6-45779785-G-A

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 0.0584 in 152,206 control chromosomes in the GnomAD database, including 468 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 0.058 (468 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.696

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.126 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: 0.0582 AC: 8852 AN: 152088 Hom.: 463 Cov.: 31

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0815

Gnomad ASJ AF: 0.0110

Gnomad EAS AF: 0.00616

Gnomad SAS AF: 0.0513

Gnomad FIN AF: 0.0207

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0241

Gnomad OTH AF: 0.0473

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

GnomAD4 genome AF: 0.0584 AC: 8891 AN: 152206 Hom.: 468 Cov.: 31 AF XY: 0.0583 AC XY: 4337 AN XY: 74436

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.0815

Gnomad4 ASJ AF: 0.0110

Gnomad4 EAS AF: 0.00598

Gnomad4 SAS AF: 0.0515

Gnomad4 FIN AF: 0.0207

Gnomad4 NFE AF: 0.0241

Gnomad4 OTH AF: 0.0468

Alfa AF: 0.0373 Hom.: 87

Bravo AF: 0.0656

Asia WGS AF: 0.0380 AC: 135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.2
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7747594; hg19: chr6-45747522;