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. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.230 AC: 9504 AN: 41384

American (AMR) AF: 0.304 AC: 4634 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 864 AN: 3466

East Asian (EAS) AF: 0.281 AC: 1452 AN: 5160

South Asian (SAS) AF: 0.285 AC: 1370 AN: 4806

European-Finnish (FIN) AF: 0.198 AC: 2083 AN: 10516

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14179 AN: 67884

Other (OTH) AF: 0.228 AC: 482 AN: 2110

Alfa AF: 0.188 Hom.: 941

Bravo AF: 0.240

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.030
DANN	Benign	0.82
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs4915414; hg19: chr1-200163003;