rs314346

Variant names:

• chr7-100800895-C-T
• rs314346

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 0.392 in 152,092 control chromosomes in the GnomAD database, including 13,931 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 0.39 (13931 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.529 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: 0.393 AC: 59706 AN: 151974 Hom.: 13945 Cov.: 31

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.0394

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.392 AC: 59681 AN: 152092 Hom.: 13931 Cov.: 31 AF XY: 0.388 AC XY: 28882 AN XY: 74346

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.412

Gnomad4 ASJ AF: 0.459

Gnomad4 EAS AF: 0.0389

Gnomad4 SAS AF: 0.343

Gnomad4 FIN AF: 0.454

Gnomad4 NFE AF: 0.534

Gnomad4 OTH AF: 0.428

Alfa AF: 0.506 Hom.: 18932

Bravo AF: 0.379

Asia WGS AF: 0.181 AC: 632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.36
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs314346; hg19: chr7-100398517;