rs10488611

Variant names:

• chr7-2480175-G-A
• rs10488611

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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 AC: 0.0468961 AN: 0.0468961

Gnomad4 AMR AF: 0.122 AC: 0.121501 AN: 0.121501

Gnomad4 ASJ AF: 0.114 AC: 0.114055 AN: 0.114055

Gnomad4 EAS AF: 0.0587 AC: 0.0587326 AN: 0.0587326

Gnomad4 SAS AF: 0.180 AC: 0.180066 AN: 0.180066

Gnomad4 FIN AF: 0.228 AC: 0.228121 AN: 0.228121

Gnomad4 NFE AF: 0.197 AC: 0.197217 AN: 0.197217

Gnomad4 OTH AF: 0.173 AC: 0.172512 AN: 0.172512

Alfa AF: 0.177 Hom.: 1345

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;