rs1604897

Variant names:

• chr8-121170070-C-T
• rs1604897

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.482 AC: 19990 AN: 41480

American (AMR) AF: 0.180 AC: 2750 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 755 AN: 3468

East Asian (EAS) AF: 0.446 AC: 2305 AN: 5166

South Asian (SAS) AF: 0.312 AC: 1502 AN: 4812

European-Finnish (FIN) AF: 0.176 AC: 1860 AN: 10586

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12588 AN: 67978

Other (OTH) AF: 0.240 AC: 507 AN: 2110

Alfa AF: 0.254 Hom.: 4526

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
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs1604897; hg19: chr8-122182310;