chr6-150059748-A-G

Variant names:

• chr6-150059748-A-G
• rs78546022

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 0.046 in 152,250 control chromosomes in the GnomAD database, including 190 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 0.046 (190 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.623
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0747 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: 0.0461 AC: 7009 AN: 152132 Hom.: 190 Cov.: 32

Gnomad AFR AF: 0.0146

Gnomad AMI AF: 0.0991

Gnomad AMR AF: 0.0501

Gnomad ASJ AF: 0.0637

Gnomad EAS AF: 0.0426

Gnomad SAS AF: 0.0813

Gnomad FIN AF: 0.0432

Gnomad MID AF: 0.0287

Gnomad NFE AF: 0.0610

Gnomad OTH AF: 0.0459

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

GnomAD4 genome AF: 0.0460 AC: 7009 AN: 152250 Hom.: 190 Cov.: 32 AF XY: 0.0462 AC XY: 3442 AN XY: 74452

African (AFR) AF: 0.0145 AC: 604 AN: 41550

American (AMR) AF: 0.0500 AC: 765 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0637 AC: 221 AN: 3470

East Asian (EAS) AF: 0.0429 AC: 222 AN: 5170

South Asian (SAS) AF: 0.0813 AC: 392 AN: 4820

European-Finnish (FIN) AF: 0.0432 AC: 459 AN: 10616

Middle Eastern (MID) AF: 0.0308 AC: 9 AN: 292

European-Non Finnish (NFE) AF: 0.0610 AC: 4151 AN: 68010

Other (OTH) AF: 0.0454 AC: 96 AN: 2114

Alfa AF: 0.0535 Hom.: 328

Bravo AF: 0.0443

Asia WGS AF: 0.0570 AC: 197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.41
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs78546022; hg19: chr6-150380884;