rs3860295

Variant names:

• chr1-206502998-G-A
• rs3860295

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 0.429 in 152,026 control chromosomes in the GnomAD database, including 14,522 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 0.43 (14522 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.726

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.609 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: 0.429 AC: 65181 AN: 151908 Hom.: 14512 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.429 AC: 65243 AN: 152026 Hom.: 14522 Cov.: 32 AF XY: 0.427 AC XY: 31721 AN XY: 74308

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.452

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.628

Gnomad4 FIN AF: 0.397

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.429

Alfa AF: 0.477 Hom.: 31947

Bravo AF: 0.423

Asia WGS AF: 0.491 AC: 1710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.46
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3860295; hg19: chr1-206676331;