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
• Publications: 3 publications found

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

African (AFR) AF: 0.0469 AC: 1949 AN: 41560

American (AMR) AF: 0.122 AC: 1858 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 396 AN: 3472

East Asian (EAS) AF: 0.0587 AC: 304 AN: 5176

South Asian (SAS) AF: 0.180 AC: 869 AN: 4826

European-Finnish (FIN) AF: 0.228 AC: 2419 AN: 10604

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13408 AN: 67986

Other (OTH) AF: 0.173 AC: 364 AN: 2110

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10488611; hg19: chr7-2519809;