chr4-122602720-G-T

Position:

• chr4-122602720-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 0.309 in 151,988 control chromosomes in the GnomAD database, including 7,985 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 0.31 (7985 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.491

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.122602720G>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46935 AN: 151868 Hom.: 7978 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.309 AC: 46959 AN: 151988 Hom.: 7985 Cov.: 32 AF XY: 0.315 AC XY: 23425 AN XY: 74280

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.396

Gnomad4 ASJ AF: 0.395

Gnomad4 EAS AF: 0.380

Gnomad4 SAS AF: 0.523

Gnomad4 FIN AF: 0.354

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.349

Alfa AF: 0.347 Hom.: 13022

Bravo AF: 0.304

Asia WGS AF: 0.437 AC: 1522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.0
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7682241; hg19: chr4-123523875;