4-170331895-G-T

Variant names:

• chr4-170331895-G-T
• rs7692005

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 0.811 in 151,772 control chromosomes in the GnomAD database, including 50,217 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 0.81 (50217 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.317
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.811 AC: 122944 AN: 151654 Hom.: 50176 Cov.: 33

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.871

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.902

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.869

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.819

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

GnomAD4 genome AF: 0.811 AC: 123041 AN: 151772 Hom.: 50217 Cov.: 33 AF XY: 0.810 AC XY: 60077 AN XY: 74162

African (AFR) AF: 0.886 AC: 36672 AN: 41380

American (AMR) AF: 0.750 AC: 11439 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.871 AC: 3020 AN: 3466

East Asian (EAS) AF: 0.994 AC: 5151 AN: 5184

South Asian (SAS) AF: 0.902 AC: 4343 AN: 4816

European-Finnish (FIN) AF: 0.751 AC: 7894 AN: 10506

Middle Eastern (MID) AF: 0.866 AC: 251 AN: 290

European-Non Finnish (NFE) AF: 0.765 AC: 51932 AN: 67858

Other (OTH) AF: 0.820 AC: 1732 AN: 2112

Alfa AF: 0.777 Hom.: 26910

Bravo AF: 0.813

Asia WGS AF: 0.940 AC: 3263 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.6
DANN	Benign	0.20
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs7692005; hg19: chr4-171253046;