rs4260611

Variant names:

• chr4-68518888-G-C
• rs4260611

Your query was ambiguous. Multiple possible variants found:

• chr4-68518888-G-C
• chr4-68518888-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.31 (12203 hom., cov: 19)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.309 AC: 38024 AN: 122998 Hom.: 12187 Cov.: 19

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.183

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.309 AC: 38066 AN: 123060 Hom.: 12203 Cov.: 19 AF XY: 0.313 AC XY: 18341 AN XY: 58564

African (AFR) AF: 0.232 AC: 8378 AN: 36182

American (AMR) AF: 0.416 AC: 4962 AN: 11922

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 811 AN: 2936

East Asian (EAS) AF: 0.393 AC: 504 AN: 1284

South Asian (SAS) AF: 0.295 AC: 761 AN: 2584

European-Finnish (FIN) AF: 0.396 AC: 2744 AN: 6926

Middle Eastern (MID) AF: 0.202 AC: 48 AN: 238

European-Non Finnish (NFE) AF: 0.326 AC: 19122 AN: 58582

Other (OTH) AF: 0.273 AC: 466 AN: 1706

Alfa AF: 0.270 Hom.: 982

Asia WGS AF: 0.247 AC: 466 AN: 1886

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.3
DANN	Benign	0.33
PhyloP100		0.23

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4260611;

hg19: chr4-69384606;