rs7407664

Positions:

• chr18-9031721-A-G
• chr18-9031721-A-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 0.0316 in 152,172 control chromosomes in the GnomAD database, including 193 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 0.032 (193 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.9031721A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0315 AC: 4794 AN: 152052 Hom.: 192 Cov.: 30

Gnomad AFR AF: 0.00790

Gnomad AMI AF: 0.00769

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.00750

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.0274

Gnomad FIN AF: 0.0153

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0342

Gnomad OTH AF: 0.0292

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

GnomAD4 genome AF: 0.0316 AC: 4804 AN: 152172 Hom.: 193 Cov.: 30 AF XY: 0.0318 AC XY: 2369 AN XY: 74392

Gnomad4 AFR AF: 0.00787

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.00750

Gnomad4 EAS AF: 0.00212

Gnomad4 SAS AF: 0.0272

Gnomad4 FIN AF: 0.0153

Gnomad4 NFE AF: 0.0342

Gnomad4 OTH AF: 0.0289

Alfa AF: 0.0145 Hom.: 10

Bravo AF: 0.0395

Asia WGS AF: 0.0230 AC: 78 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.8
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7407664; hg19: chr18-9031719;