rs6672282

chr1-79733880-G-Achr1-79733880-G-C

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 0.889 in 152,164 control chromosomes in the GnomAD database, including 60,607 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 0.89 (60607 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.889 AC: 135109 AN: 152046 Hom.: 60568 Cov.: 32

Gnomad AFR AF: 0.757

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.925

Gnomad ASJ AF: 0.938

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.863

Gnomad FIN AF: 0.965

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.943

Gnomad OTH AF: 0.884

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

GnomAD4 genome AF: 0.889 AC: 135201 AN: 152164 Hom.: 60607 Cov.: 32 AF XY: 0.889 AC XY: 66115 AN XY: 74402

Gnomad4 AFR AF: 0.757

Gnomad4 AMR AF: 0.926

Gnomad4 ASJ AF: 0.938

Gnomad4 EAS AF: 0.960

Gnomad4 SAS AF: 0.863

Gnomad4 FIN AF: 0.965

Gnomad4 NFE AF: 0.943

Gnomad4 OTH AF: 0.884

Alfa AF: 0.917 Hom.: 10863

Bravo AF: 0.881

Asia WGS AF: 0.889 AC: 3090 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.19
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6672282; hg19: chr1-80199565;