4-68812655-C-G

Variant names:

• chr4-68812655-C-G
• rs2331559

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 0.741 in 151,798 control chromosomes in the GnomAD database, including 45,870 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 0.74 (45870 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.235
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.895 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: 0.742 AC: 112480 AN: 151682 Hom.: 45863 Cov.: 30

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.817

Gnomad ASJ AF: 0.902

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.893

Gnomad FIN AF: 0.929

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.901

Gnomad OTH AF: 0.768

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

GnomAD4 genome AF: 0.741 AC: 112519 AN: 151798 Hom.: 45870 Cov.: 30 AF XY: 0.745 AC XY: 55244 AN XY: 74184

African (AFR) AF: 0.373 AC: 15411 AN: 41368

American (AMR) AF: 0.818 AC: 12422 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.902 AC: 3124 AN: 3464

East Asian (EAS) AF: 0.687 AC: 3530 AN: 5138

South Asian (SAS) AF: 0.893 AC: 4310 AN: 4826

European-Finnish (FIN) AF: 0.929 AC: 9838 AN: 10588

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.901 AC: 61186 AN: 67924

Other (OTH) AF: 0.766 AC: 1600 AN: 2090

Alfa AF: 0.814 Hom.: 6318

Bravo AF: 0.712

Asia WGS AF: 0.765 AC: 2659 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.0
DANN	Benign	0.14
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs2331559; hg19: chr4-69678373;