rs6913472

Variant names:

• chr6-52232274-G-A
• rs6913472

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 0.0808 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.0939

Gnomad4 AMR AF: 0.0544

Gnomad4 ASJ AF: 0.0446

Gnomad4 EAS AF: 0.0102

Gnomad4 SAS AF: 0.0624

Gnomad4 FIN AF: 0.0515

Gnomad4 NFE AF: 0.0913

Gnomad4 OTH AF: 0.0691

Alfa AF: 0.0848 Hom.: 254

Bravo AF: 0.0809

Asia WGS AF: 0.0420 AC: 148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6913472; hg19: chr6-52097072;