rs858249

Positions:

• chr7-23181020-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 0.0903 in 151,886 control chromosomes in the GnomAD database, including 983 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 0.090 (983 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.462

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 (AFR) allele frequency at 95% confidence interval = 0.186 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: 0.0901 AC: 13675 AN: 151768 Hom.: 973 Cov.: 31

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.00659

Gnomad AMR AF: 0.0708

Gnomad ASJ AF: 0.0663

Gnomad EAS AF: 0.0102

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0411

Gnomad OTH AF: 0.0768

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

GnomAD4 genome AF: 0.0903 AC: 13719 AN: 151886 Hom.: 983 Cov.: 31 AF XY: 0.0924 AC XY: 6859 AN XY: 74250

Gnomad4 AFR AF: 0.189

Gnomad4 AMR AF: 0.0712

Gnomad4 ASJ AF: 0.0663

Gnomad4 EAS AF: 0.0100

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.0411

Gnomad4 OTH AF: 0.0760

Alfa AF: 0.0488 Hom.: 580

Bravo AF: 0.0912

Asia WGS AF: 0.0840 AC: 291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.96
DANN	Benign	0.49

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs858249; hg19: chr7-23220639;