rs7670309

Variant names:

• chr4-69001546-G-A
• rs7670309

Your query was ambiguous. Multiple possible variants found:

• chr4-69001546-G-A
• chr4-69001546-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 0.026 (38 hom., cov: 11)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.114 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: 0.0256 AC: 2183 AN: 85274 Hom.: 37 Cov.: 11

Gnomad AFR AF: 0.0752

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0164

Gnomad ASJ AF: 0.00367

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.0193

Gnomad FIN AF: 0.000982

Gnomad MID AF: 0.0260

Gnomad NFE AF: 0.00383

Gnomad OTH AF: 0.0295

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

GnomAD4 genome AF: 0.0257 AC: 2193 AN: 85286 Hom.: 38 Cov.: 11 AF XY: 0.0252 AC XY: 1006 AN XY: 39924

African (AFR) AF: 0.0755 AC: 1592 AN: 21088

American (AMR) AF: 0.0164 AC: 128 AN: 7816

Ashkenazi Jewish (ASJ) AF: 0.00367 AC: 8 AN: 2178

East Asian (EAS) AF: 0.129 AC: 200 AN: 1550

South Asian (SAS) AF: 0.0194 AC: 53 AN: 2726

European-Finnish (FIN) AF: 0.000982 AC: 4 AN: 4074

Middle Eastern (MID) AF: 0.0294 AC: 4 AN: 136

European-Non Finnish (NFE) AF: 0.00383 AC: 168 AN: 43854

Other (OTH) AF: 0.0309 AC: 36 AN: 1164

Alfa AF: 0.0541 Hom.: 6

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.99
DANN	Benign	0.17
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs7670309; hg19: chr4-69867264;