4-154527996-T-C

Variant names:

• chr4-154527996-T-C
• rs7662567

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 0.238 in 152,104 control chromosomes in the GnomAD database, including 4,740 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 0.24 (4740 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.200
• 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 (EAS) allele frequency at 95% confidence interval = 0.533 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: 0.238 AC: 36114 AN: 151986 Hom.: 4723 Cov.: 33

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.238 AC: 36171 AN: 152104 Hom.: 4740 Cov.: 33 AF XY: 0.242 AC XY: 17992 AN XY: 74352

African (AFR) AF: 0.259 AC: 10754 AN: 41504

American (AMR) AF: 0.231 AC: 3534 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 623 AN: 3470

East Asian (EAS) AF: 0.550 AC: 2835 AN: 5152

South Asian (SAS) AF: 0.235 AC: 1132 AN: 4822

European-Finnish (FIN) AF: 0.260 AC: 2741 AN: 10558

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13742 AN: 67982

Other (OTH) AF: 0.224 AC: 473 AN: 2112

Alfa AF: 0.230 Hom.: 1041

Bravo AF: 0.238

Asia WGS AF: 0.356 AC: 1234 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	6.4
DANN	Benign	0.73
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs7662567; hg19: chr4-155449148;