chr4-68671757-A-G

Variant names:

• chr4-68671757-A-G
• rs9994887

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 0.531 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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.610 AC: 25244 AN: 41402

American (AMR) AF: 0.583 AC: 8906 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1573 AN: 3464

East Asian (EAS) AF: 0.561 AC: 2873 AN: 5118

South Asian (SAS) AF: 0.450 AC: 2161 AN: 4798

European-Finnish (FIN) AF: 0.554 AC: 5832 AN: 10536

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.477 AC: 32395 AN: 67918

Other (OTH) AF: 0.534 AC: 1123 AN: 2102

Alfa AF: 0.482 Hom.: 24647

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
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs9994887; hg19: chr4-69537475;