rs10491309

Positions:

• chr5-141299458-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 0.0648 in 152,318 control chromosomes in the GnomAD database, including 345 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 0.065 (345 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.715

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0667 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.141299458A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TAF7	ENST00000624699.1	n.128+21060T>C		intron_variant		3
TAF7	ENST00000686518.1	n.75+21060T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0649 AC: 9875 AN: 152200 Hom.: 345 Cov.: 33

Gnomad AFR AF: 0.0663

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0661

Gnomad ASJ AF: 0.0548

Gnomad EAS AF: 0.0177

Gnomad SAS AF: 0.0354

Gnomad FIN AF: 0.0741

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0684

Gnomad OTH AF: 0.0770

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

GnomAD4 genome AF: 0.0648 AC: 9877 AN: 152318 Hom.: 345 Cov.: 33 AF XY: 0.0645 AC XY: 4806 AN XY: 74488

Gnomad4 AFR AF: 0.0663

Gnomad4 AMR AF: 0.0659

Gnomad4 ASJ AF: 0.0548

Gnomad4 EAS AF: 0.0177

Gnomad4 SAS AF: 0.0354

Gnomad4 FIN AF: 0.0741

Gnomad4 NFE AF: 0.0684

Gnomad4 OTH AF: 0.0771

Alfa AF: 0.0677 Hom.: 340

Bravo AF: 0.0655

Asia WGS AF: 0.0200 AC: 72 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	16
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491309; hg19: chr5-140679023;