chr4-13007856-A-G

Variant names:

• chr4-13007856-A-G
• rs2670760

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 0.906 in 152,228 control chromosomes in the GnomAD database, including 62,515 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 0.91 (62515 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.48
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.927 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: 0.906 AC: 137798 AN: 152110 Hom.: 62462 Cov.: 32

Gnomad AFR AF: 0.916

Gnomad AMI AF: 0.902

Gnomad AMR AF: 0.940

Gnomad ASJ AF: 0.914

Gnomad EAS AF: 0.855

Gnomad SAS AF: 0.853

Gnomad FIN AF: 0.913

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.898

Gnomad OTH AF: 0.906

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

GnomAD4 genome AF: 0.906 AC: 137909 AN: 152228 Hom.: 62515 Cov.: 32 AF XY: 0.906 AC XY: 67443 AN XY: 74412

African (AFR) AF: 0.916 AC: 38044 AN: 41544

American (AMR) AF: 0.940 AC: 14386 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.914 AC: 3172 AN: 3472

East Asian (EAS) AF: 0.854 AC: 4421 AN: 5174

South Asian (SAS) AF: 0.853 AC: 4110 AN: 4820

European-Finnish (FIN) AF: 0.913 AC: 9673 AN: 10590

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.898 AC: 61103 AN: 68010

Other (OTH) AF: 0.906 AC: 1916 AN: 2114

Alfa AF: 0.895 Hom.: 9007

Bravo AF: 0.911

Asia WGS AF: 0.887 AC: 3079 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	14
DANN	Benign	0.55
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs2670760; hg19: chr4-13009480;