rs3864663

Positions:

• chr8-77768114-T-C

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 0.0973 in 152,186 control chromosomes in the GnomAD database, including 953 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 0.097 (953 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.154

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.14 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: 0.0974 AC: 14811 AN: 152068 Hom.: 955 Cov.: 32

Gnomad AFR AF: 0.0248

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.0907

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.00174

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.0972

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

GnomAD4 genome AF: 0.0973 AC: 14805 AN: 152186 Hom.: 953 Cov.: 32 AF XY: 0.0968 AC XY: 7199 AN XY: 74394

Gnomad4 AFR AF: 0.0248

Gnomad4 AMR AF: 0.0905

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.0962

Alfa AF: 0.130 Hom.: 1794

Bravo AF: 0.0887

Asia WGS AF: 0.0520 AC: 181 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3864663; hg19: chr8-78680349;