4-110021121-G-C

Variant names:

• chr4-110021121-G-C
• rs7699288

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 0.304 in 151,978 control chromosomes in the GnomAD database, including 7,187 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 0.30 (7187 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.371 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: 0.304 AC: 46204 AN: 151860 Hom.: 7171 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.304 AC: 46270 AN: 151978 Hom.: 7187 Cov.: 32 AF XY: 0.303 AC XY: 22517 AN XY: 74266

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.330

Gnomad4 EAS AF: 0.327

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.313

Alfa AF: 0.307 Hom.: 962

Bravo AF: 0.302

Asia WGS AF: 0.354 AC: 1231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.34
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7699288; hg19: chr4-110942277;