rs4468140

Variant names:

• chr1-161717095-C-A
• rs4468140

Your query was ambiguous. Multiple possible variants found:

• chr1-161717095-C-A
• chr1-161717095-C-G

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 0.0481 in 152,242 control chromosomes in the GnomAD database, including 582 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 0.048 (582 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.529
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.382 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: 0.0481 AC: 7314 AN: 152124 Hom.: 580 Cov.: 32

Gnomad AFR AF: 0.0647

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0279

Gnomad ASJ AF: 0.0150

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.0288

Gnomad FIN AF: 0.0192

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0245

Gnomad OTH AF: 0.0420

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

GnomAD4 genome AF: 0.0481 AC: 7325 AN: 152242 Hom.: 582 Cov.: 32 AF XY: 0.0484 AC XY: 3600 AN XY: 74432

African (AFR) AF: 0.0649 AC: 2694 AN: 41534

American (AMR) AF: 0.0278 AC: 426 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0150 AC: 52 AN: 3468

East Asian (EAS) AF: 0.396 AC: 2050 AN: 5176

South Asian (SAS) AF: 0.0282 AC: 136 AN: 4820

European-Finnish (FIN) AF: 0.0192 AC: 204 AN: 10604

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0245 AC: 1669 AN: 68020

Other (OTH) AF: 0.0411 AC: 87 AN: 2116

Alfa AF: 0.0406 Hom.: 43

Bravo AF: 0.0532

Asia WGS AF: 0.157 AC: 546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.7
DANN	Benign	0.81
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs4468140; hg19: chr1-161686885;