rs7224319

Positions:

• chr17-41001135-G-A

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 0.233 in 152,122 control chromosomes in the GnomAD database, including 6,929 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 0.23 (6929 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.588

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.41001135G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35412 AN: 152004 Hom.: 6896 Cov.: 33

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.0775

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0898

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.233 AC: 35490 AN: 152122 Hom.: 6929 Cov.: 33 AF XY: 0.234 AC XY: 17378 AN XY: 74362

Gnomad4 AFR AF: 0.534

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.0775

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.0898

Gnomad4 OTH AF: 0.203

Alfa AF: 0.154 Hom.: 489

Bravo AF: 0.256

Asia WGS AF: 0.238 AC: 828 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.53
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7224319; hg19: chr17-39157387;