5-56738380-A-G

Variant names:

• chr5-56738380-A-G
• rs4700485

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 0.712 in 152,030 control chromosomes in the GnomAD database, including 38,880 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 0.71 (38880 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.344
• Publications: 21 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.712 AC: 108153 AN: 151912 Hom.: 38854 Cov.: 31

Gnomad AFR AF: 0.764

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.767

Gnomad MID AF: 0.686

Gnomad NFE AF: 0.721

Gnomad OTH AF: 0.698

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

GnomAD4 genome AF: 0.712 AC: 108213 AN: 152030 Hom.: 38880 Cov.: 31 AF XY: 0.707 AC XY: 52496 AN XY: 74296

African (AFR) AF: 0.764 AC: 31669 AN: 41460

American (AMR) AF: 0.624 AC: 9538 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 2376 AN: 3470

East Asian (EAS) AF: 0.449 AC: 2316 AN: 5156

South Asian (SAS) AF: 0.611 AC: 2946 AN: 4818

European-Finnish (FIN) AF: 0.767 AC: 8097 AN: 10558

Middle Eastern (MID) AF: 0.679 AC: 197 AN: 290

European-Non Finnish (NFE) AF: 0.721 AC: 48994 AN: 67968

Other (OTH) AF: 0.694 AC: 1468 AN: 2116

Alfa AF: 0.710 Hom.: 79335

Bravo AF: 0.703

Asia WGS AF: 0.553 AC: 1923 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.3
DANN	Benign	0.66
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs4700485; hg19: chr5-56034207; COSMIC: COSV69628567;