13-107120051-G-T

Variant names:

• chr13-107120051-G-T
• rs713548

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 0.264 in 151,994 control chromosomes in the GnomAD database, including 5,578 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 0.26 (5578 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.430
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40170 AN: 151876 Hom.: 5583 Cov.: 33

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.264 AC: 40186 AN: 151994 Hom.: 5578 Cov.: 33 AF XY: 0.268 AC XY: 19915 AN XY: 74274

African (AFR) AF: 0.327 AC: 13541 AN: 41438

American (AMR) AF: 0.200 AC: 3052 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 885 AN: 3468

East Asian (EAS) AF: 0.400 AC: 2068 AN: 5166

South Asian (SAS) AF: 0.329 AC: 1585 AN: 4814

European-Finnish (FIN) AF: 0.299 AC: 3156 AN: 10558

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.225 AC: 15263 AN: 67958

Other (OTH) AF: 0.232 AC: 490 AN: 2114

Alfa AF: 0.231 Hom.: 4978

Bravo AF: 0.257

Asia WGS AF: 0.365 AC: 1265 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.3
DANN	Benign	0.44
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs713548; hg19: chr13-107772399;