chr7-56205683-G-T

Variant names:

• chr7-56205683-G-T
• rs1404223

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 0.157 in 152,106 control chromosomes in the GnomAD database, including 2,026 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 0.16 (2026 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.386 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: 0.157 AC: 23909 AN: 151988 Hom.: 2023 Cov.: 33

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.157 AC: 23923 AN: 152106 Hom.: 2026 Cov.: 33 AF XY: 0.161 AC XY: 11966 AN XY: 74350

African (AFR) AF: 0.146 AC: 6049 AN: 41500

American (AMR) AF: 0.148 AC: 2259 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 404 AN: 3468

East Asian (EAS) AF: 0.401 AC: 2070 AN: 5166

South Asian (SAS) AF: 0.129 AC: 622 AN: 4828

European-Finnish (FIN) AF: 0.202 AC: 2131 AN: 10550

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 9965 AN: 68000

Other (OTH) AF: 0.143 AC: 301 AN: 2112

Alfa AF: 0.0824 Hom.: 139

Bravo AF: 0.156

Asia WGS AF: 0.238 AC: 827 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	4.3
DANN	Benign	0.53
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs1404223; hg19: chr7-56273376;