rs9312101

chr4-63016167-C-T

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 0.196 in 152,010 control chromosomes in the GnomAD database, including 3,300 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 0.20 (3300 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.415

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29718 AN: 151890 Hom.: 3298 Cov.: 32

Gnomad AFR AF: 0.0852

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.196 AC: 29724 AN: 152010 Hom.: 3300 Cov.: 32 AF XY: 0.196 AC XY: 14535 AN XY: 74296

Gnomad4 AFR AF: 0.0852

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.215

Alfa AF: 0.216 Hom.: 493

Bravo AF: 0.196

Asia WGS AF: 0.177 AC: 615 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	8.0
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9312101; hg19: chr4-63881885;