rs1604897

Positions:

• chr8-121170070-C-T

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 0.279 in 152,086 control chromosomes in the GnomAD database, including 7,306 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 0.28 (7306 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.696

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42406 AN: 151966 Hom.: 7285 Cov.: 32

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.279 AC: 42473 AN: 152086 Hom.: 7306 Cov.: 32 AF XY: 0.278 AC XY: 20684 AN XY: 74344

Gnomad4 AFR AF: 0.482

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.240

Alfa AF: 0.213 Hom.: 1805

Bravo AF: 0.285

Asia WGS AF: 0.346 AC: 1201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	13
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1604897; hg19: chr8-122182310;