rs2865703

Variant names:

• chr4-95726437-T-C
• rs2865703

Your query was ambiguous. Multiple possible variants found:

• chr4-95726437-T-C
• chr4-95726437-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 0.728 in 152,160 control chromosomes in the GnomAD database, including 42,576 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 0.73 (42576 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.37
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.871 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: 0.728 AC: 110704 AN: 152042 Hom.: 42557 Cov.: 33

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.907

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.863

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.877

Gnomad OTH AF: 0.737

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

GnomAD4 genome AF: 0.728 AC: 110761 AN: 152160 Hom.: 42576 Cov.: 33 AF XY: 0.722 AC XY: 53724 AN XY: 74372

African (AFR) AF: 0.491 AC: 20350 AN: 41476

American (AMR) AF: 0.670 AC: 10241 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.719 AC: 2494 AN: 3470

East Asian (EAS) AF: 0.627 AC: 3237 AN: 5162

South Asian (SAS) AF: 0.637 AC: 3071 AN: 4822

European-Finnish (FIN) AF: 0.863 AC: 9156 AN: 10606

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.877 AC: 59627 AN: 68024

Other (OTH) AF: 0.738 AC: 1556 AN: 2108

Alfa AF: 0.820 Hom.: 28200

Bravo AF: 0.707

Asia WGS AF: 0.580 AC: 2022 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.14
DANN	Benign	0.82
PhyloP100		-3.4

Splicing

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

Other links and lift over

dbSNP: rs2865703; hg19: chr4-96647588;