chr5-68418419-A-G

Variant names:

• chr5-68418419-A-G
• rs4976033

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 0.494 in 152,058 control chromosomes in the GnomAD database, including 19,840 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 0.49 (19840 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00900
• Publications: 29 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.494 AC: 75035 AN: 151940 Hom.: 19829 Cov.: 31

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.494 AC: 75088 AN: 152058 Hom.: 19840 Cov.: 31 AF XY: 0.491 AC XY: 36491 AN XY: 74342

African (AFR) AF: 0.679 AC: 28155 AN: 41458

American (AMR) AF: 0.487 AC: 7435 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1424 AN: 3468

East Asian (EAS) AF: 0.522 AC: 2703 AN: 5178

South Asian (SAS) AF: 0.323 AC: 1554 AN: 4814

European-Finnish (FIN) AF: 0.389 AC: 4122 AN: 10588

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.415 AC: 28187 AN: 67964

Other (OTH) AF: 0.479 AC: 1011 AN: 2110

Alfa AF: 0.439 Hom.: 56965

Bravo AF: 0.506

Asia WGS AF: 0.398 AC: 1385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.8
DANN	Benign	0.42
PhyloP100		-0.0090

Splicing

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

Other links and lift over

dbSNP: rs4976033; hg19: chr5-67714246;