rs316636

Variant names:

• chr1-84286783-G-C
• rs316636

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;