rs1364616

Variant names:

• chr8-71654009-C-A
• rs1364616

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;