rs3898608

Variant names:

• chr1-221524373-T-C
• rs3898608

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 0.294 in 148,504 control chromosomes in the GnomAD database, including 6,965 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 0.29 (6965 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.270

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.403 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: 0.295 AC: 43720 AN: 148392 Hom.: 6966 Cov.: 27

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.294 AC: 43725 AN: 148504 Hom.: 6965 Cov.: 27 AF XY: 0.299 AC XY: 21649 AN XY: 72412

Gnomad4 AFR AF: 0.210

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.372

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.308

Alfa AF: 0.298 Hom.: 856

Bravo AF: 0.287

Asia WGS AF: 0.317 AC: 1082 AN: 3418

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.5
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3898608; hg19: chr1-221697715; COSMIC: COSV53384024;