rs4915414

Variant names:

• chr1-200193875-G-A
• rs4915414

Your query was ambiguous. Multiple possible variants found:

• chr1-200193875-G-A
• chr1-200193875-G-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 0.23 in 151,770 control chromosomes in the GnomAD database, including 4,119 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 0.23 (4119 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18

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 (AMR) allele frequency at 95% confidence interval = 0.297 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: 0.230 AC: 34827 AN: 151652 Hom.: 4109 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.230 AC: 34871 AN: 151770 Hom.: 4119 Cov.: 32 AF XY: 0.230 AC XY: 17089 AN XY: 74164

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.228

Alfa AF: 0.157 Hom.: 406

Bravo AF: 0.240

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.030
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: rs4915414; hg19: chr1-200163003;