chr4-6889792-G-C

Position:

• chr4-6889792-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.173 in 152,220 control chromosomes in the GnomAD database, including 2,742 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 0.17 (2742 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.361

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26287 AN: 152104 Hom.: 2742 Cov.: 33

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.173 AC: 26284 AN: 152220 Hom.: 2742 Cov.: 33 AF XY: 0.174 AC XY: 12960 AN XY: 74424

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.557

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.175

Alfa AF: 0.185 Hom.: 1722

Bravo AF: 0.175

Asia WGS AF: 0.266 AC: 926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.8
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11734132; hg19: chr4-6891519;