rs13272568

Positions:

• chr8-78122224-C-A
• chr8-78122224-C-G

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 0.442 in 151,878 control chromosomes in the GnomAD database, including 15,351 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 0.44 (15351 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.525

ACMG classification

Verdict is Benign. Variant got -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 = 0.509 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.442 AC: 67057 AN: 151760 Hom.: 15323 Cov.: 32

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.442 AC: 67127 AN: 151878 Hom.: 15351 Cov.: 32 AF XY: 0.435 AC XY: 32289 AN XY: 74214

Gnomad4 AFR AF: 0.515

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.448

Gnomad4 OTH AF: 0.434

Alfa AF: 0.399 Hom.: 2972

Bravo AF: 0.437

Asia WGS AF: 0.322 AC: 1123 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	0.17
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13272568; hg19: chr8-79034459;