rs1662845

chr4-81233128-A-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 0.581 in 151,968 control chromosomes in the GnomAD database, including 28,842 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 0.58 (28842 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.89 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88227 AN: 151850 Hom.: 28781 Cov.: 31

Gnomad AFR AF: 0.898

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.581 AC: 88345 AN: 151968 Hom.: 28842 Cov.: 31 AF XY: 0.578 AC XY: 42881 AN XY: 74244

Gnomad4 AFR AF: 0.898

Gnomad4 AMR AF: 0.573

Gnomad4 ASJ AF: 0.556

Gnomad4 EAS AF: 0.462

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.560

Alfa AF: 0.526 Hom.: 2889

Bravo AF: 0.610

Asia WGS AF: 0.472 AC: 1644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.35
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1662845; hg19: chr4-82154282;