rs3860295

Variant names:

• chr1-206502998-G-A
• rs3860295

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 18 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.325 AC: 13470 AN: 41486

American (AMR) AF: 0.451 AC: 6899 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1569 AN: 3470

East Asian (EAS) AF: 0.381 AC: 1966 AN: 5166

South Asian (SAS) AF: 0.628 AC: 3025 AN: 4820

European-Finnish (FIN) AF: 0.397 AC: 4194 AN: 10566

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.482 AC: 32740 AN: 67918

Other (OTH) AF: 0.429 AC: 905 AN: 2110

Alfa AF: 0.466 Hom.: 71229

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
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs3860295; hg19: chr1-206676331;