rs4732556

Variant names:

• chr7-84494923-T-A
• rs4732556

Your query was ambiguous. Multiple possible variants found:

• chr7-84494923-T-A
• chr7-84494923-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.00164

Gnomad4 AMR AF: 0.0410

Gnomad4 ASJ AF: 0.0196

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.0104

Gnomad4 FIN AF: 0.0103

Gnomad4 NFE AF: 0.00391

Gnomad4 OTH AF: 0.0166

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4732556; hg19: chr7-84124239;