rs10488611

Positions:

• chr7-2480175-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 0.143 in 152,232 control chromosomes in the GnomAD database, including 2,035 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 0.14 (2035 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

Genes affected

(HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.2480175G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21802 AN: 152114 Hom.: 2029 Cov.: 33

Gnomad AFR AF: 0.0469

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.0588

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.143 AC: 21819 AN: 152232 Hom.: 2035 Cov.: 33 AF XY: 0.144 AC XY: 10705 AN XY: 74424

Gnomad4 AFR AF: 0.0469

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.0587

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.228

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.173

Alfa AF: 0.177 Hom.: 1215

Bravo AF: 0.130

Asia WGS AF: 0.137 AC: 475 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	1.1
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10488611; hg19: chr7-2519809;