rs9994887

Positions:

• chr4-68671757-A-G
• chr4-68671757-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 0.531 in 151,814 control chromosomes in the GnomAD database, including 21,870 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 0.53 (21870 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.820

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.603 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: 0.531 AC: 80576 AN: 151694 Hom.: 21819 Cov.: 30

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.531 AC: 80684 AN: 151814 Hom.: 21870 Cov.: 30 AF XY: 0.534 AC XY: 39636 AN XY: 74156

Gnomad4 AFR AF: 0.610

Gnomad4 AMR AF: 0.583

Gnomad4 ASJ AF: 0.454

Gnomad4 EAS AF: 0.561

Gnomad4 SAS AF: 0.450

Gnomad4 FIN AF: 0.554

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.534

Alfa AF: 0.483 Hom.: 14705

Bravo AF: 0.538

Asia WGS AF: 0.488 AC: 1699 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.3
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9994887; hg19: chr4-69537475;