chr4-96959258-C-T

Variant names:

• chr4-96959258-C-T
• rs7694207

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 0.281 in 152,052 control chromosomes in the GnomAD database, including 6,872 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 0.28 (6872 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

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 (AFR) allele frequency at 95% confidence interval = 0.421 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: 0.281 AC: 42700 AN: 151934 Hom.: 6851 Cov.: 33

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.281 AC: 42748 AN: 152052 Hom.: 6872 Cov.: 33 AF XY: 0.279 AC XY: 20719 AN XY: 74328

Gnomad4 AFR AF: 0.427

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.311

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.310

Alfa AF: 0.249 Hom.: 8439

Bravo AF: 0.293

Asia WGS AF: 0.237 AC: 824 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.93
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7694207; hg19: chr4-97880409;