rs4698000

Variant names:

• chr4-10275843-T-C
• rs4698000

Your query was ambiguous. Multiple possible variants found:

• chr4-10275843-T-C
• chr4-10275843-T-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 0.677 in 152,108 control chromosomes in the GnomAD database, including 35,034 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 0.68 (35034 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.701 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: 0.677 AC: 102885 AN: 151990 Hom.: 35008 Cov.: 33

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.700

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

GnomAD4 genome AF: 0.677 AC: 102958 AN: 152108 Hom.: 35034 Cov.: 33 AF XY: 0.676 AC XY: 50238 AN XY: 74346

African (AFR) AF: 0.674 AC: 27983 AN: 41492

American (AMR) AF: 0.681 AC: 10408 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.793 AC: 2754 AN: 3472

East Asian (EAS) AF: 0.507 AC: 2608 AN: 5144

South Asian (SAS) AF: 0.721 AC: 3479 AN: 4824

European-Finnish (FIN) AF: 0.648 AC: 6871 AN: 10596

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.685 AC: 46581 AN: 67982

Other (OTH) AF: 0.697 AC: 1473 AN: 2112

Alfa AF: 0.657 Hom.: 6398

Bravo AF: 0.680

Asia WGS AF: 0.627 AC: 2179 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.51
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs4698000; hg19: chr4-10277467;