rs982723

chr18-7547609-A-G

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 0.062 in 151,846 control chromosomes in the GnomAD database, including 410 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 0.062 (410 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0620 AC: 9405 AN: 151728 Hom.: 409 Cov.: 32

Gnomad AFR AF: 0.0941

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0418

Gnomad ASJ AF: 0.0589

Gnomad EAS AF: 0.0818

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.0378

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0401

Gnomad OTH AF: 0.0626

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

GnomAD4 genome AF: 0.0620 AC: 9414 AN: 151846 Hom.: 410 Cov.: 32 AF XY: 0.0648 AC XY: 4808 AN XY: 74222

Gnomad4 AFR AF: 0.0940

Gnomad4 AMR AF: 0.0417

Gnomad4 ASJ AF: 0.0589

Gnomad4 EAS AF: 0.0824

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.0378

Gnomad4 NFE AF: 0.0401

Gnomad4 OTH AF: 0.0620

Alfa AF: 0.0473 Hom.: 284

Bravo AF: 0.0597

Asia WGS AF: 0.141 AC: 491 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.36
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs982723; hg19: chr18-7547607;