chr4-170048648-C-T

Variant names:

• chr4-170048648-C-T
• rs7694879

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 0.0608 in 152,230 control chromosomes in the GnomAD database, including 383 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 0.061 (383 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.09 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: 0.0608 AC: 9253 AN: 152112 Hom.: 382 Cov.: 32

Gnomad AFR AF: 0.0169

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.0597

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.0752

Gnomad FIN AF: 0.0404

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0919

Gnomad OTH AF: 0.0686

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

GnomAD4 genome AF: 0.0608 AC: 9254 AN: 152230 Hom.: 383 Cov.: 32 AF XY: 0.0578 AC XY: 4299 AN XY: 74418

African (AFR) AF: 0.0168 AC: 696 AN: 41518

American (AMR) AF: 0.0594 AC: 909 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 394 AN: 3472

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5184

South Asian (SAS) AF: 0.0765 AC: 369 AN: 4826

European-Finnish (FIN) AF: 0.0404 AC: 428 AN: 10594

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0919 AC: 6254 AN: 68030

Other (OTH) AF: 0.0679 AC: 143 AN: 2106

Alfa AF: 0.0324 Hom.: 25

Bravo AF: 0.0590

Asia WGS AF: 0.0350 AC: 122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.8
DANN	Benign	0.53
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs7694879; hg19: chr4-170969799;