chr4-13008468-C-T

Variant names:

• chr4-13008468-C-T
• rs2056117

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.329 in 152,010 control chromosomes in the GnomAD database, including 8,482 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 0.33 (8482 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.26
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.4 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: 0.329 AC: 49987 AN: 151892 Hom.: 8475 Cov.: 32

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.329 AC: 50006 AN: 152010 Hom.: 8482 Cov.: 32 AF XY: 0.328 AC XY: 24329 AN XY: 74274

African (AFR) AF: 0.281 AC: 11642 AN: 41456

American (AMR) AF: 0.275 AC: 4205 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 814 AN: 3470

East Asian (EAS) AF: 0.287 AC: 1485 AN: 5166

South Asian (SAS) AF: 0.415 AC: 1998 AN: 4816

European-Finnish (FIN) AF: 0.346 AC: 3643 AN: 10542

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.370 AC: 25163 AN: 67962

Other (OTH) AF: 0.303 AC: 641 AN: 2116

Alfa AF: 0.338 Hom.: 1660

Bravo AF: 0.317

Asia WGS AF: 0.365 AC: 1269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	19
DANN	Benign	0.78
PhyloP100		2.3

Splicing

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

Other links and lift over

dbSNP: rs2056117; hg19: chr4-13010092;