rs316636

Positions:

• chr1-84286783-G-C
• chr1-84286783-G-T

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 0.78 in 152,124 control chromosomes in the GnomAD database, including 46,963 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 0.78 (46963 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.591

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 = 0.976 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: 0.780 AC: 118534 AN: 152006 Hom.: 46946 Cov.: 32

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.866

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.881

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.869

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.829

Gnomad OTH AF: 0.789

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

GnomAD4 genome AF: 0.780 AC: 118589 AN: 152124 Hom.: 46963 Cov.: 32 AF XY: 0.781 AC XY: 58118 AN XY: 74392

Gnomad4 AFR AF: 0.636

Gnomad4 AMR AF: 0.791

Gnomad4 ASJ AF: 0.881

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.870

Gnomad4 FIN AF: 0.814

Gnomad4 NFE AF: 0.829

Gnomad4 OTH AF: 0.789

Alfa AF: 0.792 Hom.: 5991

Bravo AF: 0.770

Asia WGS AF: 0.910 AC: 3162 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	0.85
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs316636; hg19: chr1-84752466;