rs1648707

Variant names:

• chr3-186833922-A-C
• rs1648707

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 0.43 in 151,606 control chromosomes in the GnomAD database, including 14,916 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 (14916 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.515

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.537 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: 0.430 AC: 65104 AN: 151488 Hom.: 14897 Cov.: 30

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.430 AC: 65170 AN: 151606 Hom.: 14916 Cov.: 30 AF XY: 0.440 AC XY: 32583 AN XY: 74060

Gnomad4 AFR AF: 0.543

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.481

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.602

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.375

Alfa AF: 0.350 Hom.: 14306

Bravo AF: 0.423

Asia WGS AF: 0.447 AC: 1560 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.88
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1648707; hg19: chr3-186551711;