rs3896439

Positions:

• chr1-4608610-G-A
• chr1-4608610-G-C

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 0.0955 in 151,932 control chromosomes in the GnomAD database, including 1,044 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 0.095 (1044 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.539

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0953 AC: 14475 AN: 151814 Hom.: 1038 Cov.: 29

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.00440

Gnomad AMR AF: 0.0500

Gnomad ASJ AF: 0.0942

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.0811

Gnomad FIN AF: 0.0787

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0481

Gnomad OTH AF: 0.0901

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

GnomAD4 genome AF: 0.0955 AC: 14503 AN: 151932 Hom.: 1044 Cov.: 29 AF XY: 0.0971 AC XY: 7206 AN XY: 74232

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.0498

Gnomad4 ASJ AF: 0.0942

Gnomad4 EAS AF: 0.332

Gnomad4 SAS AF: 0.0799

Gnomad4 FIN AF: 0.0787

Gnomad4 NFE AF: 0.0480

Gnomad4 OTH AF: 0.0939

Alfa AF: 0.0579 Hom.: 870

Bravo AF: 0.0955

Asia WGS AF: 0.214 AC: 744 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	13
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3896439; hg19: chr1-4668670;