chr7-56205683-G-T

Position:

• chr7-56205683-G-T

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 0.157 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.56205683G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.401

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.143

Alfa AF: 0.0799 Hom.: 132

Bravo AF: 0.156

Asia WGS AF: 0.238 AC: 827 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1404223; hg19: chr7-56273376;