7-7321892-G-T

Position:

• chr7-7321892-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 0.521 in 152,012 control chromosomes in the GnomAD database, including 23,341 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 0.52 (23341 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.01

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.7321892G>T		intergenic_region
LOC107986764	XR_002956539.2	n.441+50048G>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.522 AC: 79230 AN: 151894 Hom.: 23328 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.521 AC: 79261 AN: 152012 Hom.: 23341 Cov.: 32 AF XY: 0.526 AC XY: 39051 AN XY: 74266

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.591

Gnomad4 ASJ AF: 0.688

Gnomad4 EAS AF: 0.734

Gnomad4 SAS AF: 0.664

Gnomad4 FIN AF: 0.625

Gnomad4 NFE AF: 0.633

Gnomad4 OTH AF: 0.545

Alfa AF: 0.605 Hom.: 24425

Bravo AF: 0.508

Asia WGS AF: 0.690 AC: 2398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1882600; hg19: chr7-7361523;