chr7-84494923-T-A

Variant names:

• chr7-84494923-T-A
• rs4732556

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 0.0134 in 152,124 control chromosomes in the GnomAD database, including 96 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 0.013 (96 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.112
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0134 AC: 2040 AN: 152006 Hom.: 96 Cov.: 32

Gnomad AFR AF: 0.00164

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0412

Gnomad ASJ AF: 0.0196

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.0106

Gnomad FIN AF: 0.0103

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00391

Gnomad OTH AF: 0.0172

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

GnomAD4 genome AF: 0.0134 AC: 2036 AN: 152124 Hom.: 96 Cov.: 32 AF XY: 0.0149 AC XY: 1109 AN XY: 74350

African (AFR) AF: 0.00164 AC: 68 AN: 41550

American (AMR) AF: 0.0410 AC: 626 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0196 AC: 68 AN: 3464

East Asian (EAS) AF: 0.158 AC: 811 AN: 5146

South Asian (SAS) AF: 0.0104 AC: 50 AN: 4824

European-Finnish (FIN) AF: 0.0103 AC: 109 AN: 10618

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00391 AC: 266 AN: 67946

Other (OTH) AF: 0.0166 AC: 35 AN: 2112

Alfa AF: 0.00321 Hom.: 1

Bravo AF: 0.0166

Asia WGS AF: 0.0720 AC: 251 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.14
DANN	Benign	0.56
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs4732556; hg19: chr7-84124239;