rs6662618

chr1-92469854-T-G

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 0.758 in 152,074 control chromosomes in the GnomAD database, including 45,011 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 0.76 (45011 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.95 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: 0.759 AC: 115304 AN: 151956 Hom.: 45007 Cov.: 33

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.945

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.753

Gnomad EAS AF: 0.972

Gnomad SAS AF: 0.856

Gnomad FIN AF: 0.859

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.837

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.758 AC: 115336 AN: 152074 Hom.: 45011 Cov.: 33 AF XY: 0.760 AC XY: 56480 AN XY: 74360

Gnomad4 AFR AF: 0.568

Gnomad4 AMR AF: 0.744

Gnomad4 ASJ AF: 0.753

Gnomad4 EAS AF: 0.973

Gnomad4 SAS AF: 0.855

Gnomad4 FIN AF: 0.859

Gnomad4 NFE AF: 0.837

Gnomad4 OTH AF: 0.747

Alfa AF: 0.818 Hom.: 68464

Bravo AF: 0.743

Asia WGS AF: 0.884 AC: 3066 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	3.6
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6662618; hg19: chr1-92935411;