rs778334

Variant names:

• chr13-105507319-G-A
• rs778334

Your query was ambiguous. Multiple possible variants found:

• chr13-105507319-G-A
• chr13-105507319-G-T

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 0.149 in 151,986 control chromosomes in the GnomAD database, including 1,905 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 0.15 (1905 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.03
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.318 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: 0.149 AC: 22697 AN: 151868 Hom.: 1900 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.0898

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.149 AC: 22721 AN: 151986 Hom.: 1905 Cov.: 32 AF XY: 0.149 AC XY: 11034 AN XY: 74274

African (AFR) AF: 0.155 AC: 6446 AN: 41460

American (AMR) AF: 0.0896 AC: 1369 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 419 AN: 3472

East Asian (EAS) AF: 0.251 AC: 1291 AN: 5144

South Asian (SAS) AF: 0.332 AC: 1600 AN: 4820

European-Finnish (FIN) AF: 0.125 AC: 1314 AN: 10540

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9905 AN: 67956

Other (OTH) AF: 0.144 AC: 305 AN: 2112

Alfa AF: 0.0783 Hom.: 113

Bravo AF: 0.142

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.054
DANN	Benign	0.36
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs778334; hg19: chr13-106159668;