rs4076635

Variant names:

• chr1-5170686-G-A
• rs4076635

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 0.388 in 152,066 control chromosomes in the GnomAD database, including 11,652 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 0.39 (11652 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.339
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.412 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: 0.388 AC: 58972 AN: 151948 Hom.: 11647 Cov.: 32

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.388 AC: 59003 AN: 152066 Hom.: 11652 Cov.: 32 AF XY: 0.386 AC XY: 28702 AN XY: 74342

African (AFR) AF: 0.351 AC: 14552 AN: 41462

American (AMR) AF: 0.363 AC: 5543 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.530 AC: 1839 AN: 3472

East Asian (EAS) AF: 0.275 AC: 1416 AN: 5154

South Asian (SAS) AF: 0.315 AC: 1520 AN: 4818

European-Finnish (FIN) AF: 0.422 AC: 4462 AN: 10584

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.417 AC: 28310 AN: 67968

Other (OTH) AF: 0.412 AC: 872 AN: 2114

Alfa AF: 0.398 Hom.: 4555

Bravo AF: 0.384

Asia WGS AF: 0.296 AC: 1032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.69
PhyloP100		-0.34

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: rs4076635;

hg19: chr1-5230746;