4-154980451-A-G

Variant names:

• chr4-154980451-A-G
• rs7687314

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 0.666 in 152,028 control chromosomes in the GnomAD database, including 35,383 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 0.67 (35383 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 3 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 (AFR) allele frequency at 95% confidence interval = 0.887 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: 0.666 AC: 101127 AN: 151912 Hom.: 35324 Cov.: 33

Gnomad AFR AF: 0.895

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.666 AC: 101237 AN: 152028 Hom.: 35383 Cov.: 33 AF XY: 0.666 AC XY: 49478 AN XY: 74296

African (AFR) AF: 0.895 AC: 37090 AN: 41450

American (AMR) AF: 0.600 AC: 9165 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.575 AC: 1995 AN: 3468

East Asian (EAS) AF: 0.745 AC: 3846 AN: 5164

South Asian (SAS) AF: 0.715 AC: 3448 AN: 4820

European-Finnish (FIN) AF: 0.602 AC: 6361 AN: 10562

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.547 AC: 37208 AN: 67962

Other (OTH) AF: 0.632 AC: 1337 AN: 2114

Alfa AF: 0.647 Hom.: 6033

Bravo AF: 0.673

Asia WGS AF: 0.700 AC: 2431 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.59
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs7687314; hg19: chr4-155901603;