rs7314777

Variant names:

• chr12-68256855-T-C
• rs7314777

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.191 in 151,484 control chromosomes in the GnomAD database, including 2,950 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 0.19 (2950 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.302
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.235 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: 0.191 AC: 28922 AN: 151366 Hom.: 2950 Cov.: 31

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.191 AC: 28944 AN: 151484 Hom.: 2950 Cov.: 31 AF XY: 0.195 AC XY: 14456 AN XY: 73994

African (AFR) AF: 0.239 AC: 9859 AN: 41242

American (AMR) AF: 0.163 AC: 2478 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 676 AN: 3470

East Asian (EAS) AF: 0.103 AC: 532 AN: 5150

South Asian (SAS) AF: 0.134 AC: 643 AN: 4800

European-Finnish (FIN) AF: 0.308 AC: 3214 AN: 10432

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10859 AN: 67878

Other (OTH) AF: 0.190 AC: 399 AN: 2100

Alfa AF: 0.169 Hom.: 289

Bravo AF: 0.187

Asia WGS AF: 0.152 AC: 527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.0
DANN	Benign	0.61
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs7314777; hg19: chr12-68650635;