rs1364616

Positions:

• chr8-71654009-C-A

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 0.386 in 151,916 control chromosomes in the GnomAD database, including 12,560 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 0.39 (12560 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.473

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.51 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: 0.386 AC: 58552 AN: 151798 Hom.: 12561 Cov.: 31

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.648

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.386 AC: 58574 AN: 151916 Hom.: 12560 Cov.: 31 AF XY: 0.383 AC XY: 28462 AN XY: 74240

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.378

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.527

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.496

Gnomad4 NFE AF: 0.481

Gnomad4 OTH AF: 0.340

Alfa AF: 0.442 Hom.: 20392

Bravo AF: 0.371

Asia WGS AF: 0.371 AC: 1290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	5.6
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1364616; hg19: chr8-72566244;