rs6913472

Variant names:

• chr6-52232274-G-A
• rs6913472

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 0.0808 in 152,184 control chromosomes in the GnomAD database, including 565 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 0.081 (565 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.340
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0915 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0808 AC: 12286 AN: 152066 Hom.: 564 Cov.: 32

Gnomad AFR AF: 0.0939

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.0545

Gnomad ASJ AF: 0.0446

Gnomad EAS AF: 0.0104

Gnomad SAS AF: 0.0626

Gnomad FIN AF: 0.0515

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0913

Gnomad OTH AF: 0.0694

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

GnomAD4 genome AF: 0.0808 AC: 12292 AN: 152184 Hom.: 565 Cov.: 32 AF XY: 0.0774 AC XY: 5759 AN XY: 74412

African (AFR) AF: 0.0939 AC: 3898 AN: 41504

American (AMR) AF: 0.0544 AC: 831 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0446 AC: 155 AN: 3472

East Asian (EAS) AF: 0.0102 AC: 53 AN: 5190

South Asian (SAS) AF: 0.0624 AC: 301 AN: 4822

European-Finnish (FIN) AF: 0.0515 AC: 545 AN: 10592

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0913 AC: 6211 AN: 68002

Other (OTH) AF: 0.0691 AC: 146 AN: 2112

Alfa AF: 0.0851 Hom.: 363

Bravo AF: 0.0809

Asia WGS AF: 0.0420 AC: 148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.6
DANN	Benign	0.82
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs6913472; hg19: chr6-52097072;