rs10487574

Variant names:

• chr7-48735652-A-G
• rs10487574

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 0.136 in 152,232 control chromosomes in the GnomAD database, including 1,517 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 (1517 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.438
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.154 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: 0.136 AC: 20656 AN: 152114 Hom.: 1517 Cov.: 33

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.0625

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.136 AC: 20671 AN: 152232 Hom.: 1517 Cov.: 33 AF XY: 0.133 AC XY: 9897 AN XY: 74436

African (AFR) AF: 0.113 AC: 4692 AN: 41532

American (AMR) AF: 0.150 AC: 2296 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 440 AN: 3466

East Asian (EAS) AF: 0.0625 AC: 324 AN: 5186

South Asian (SAS) AF: 0.117 AC: 567 AN: 4828

European-Finnish (FIN) AF: 0.108 AC: 1150 AN: 10602

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10614 AN: 68014

Other (OTH) AF: 0.145 AC: 307 AN: 2116

Alfa AF: 0.149 Hom.: 1135

Bravo AF: 0.137

Asia WGS AF: 0.0960 AC: 335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.35
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs10487574; hg19: chr7-48775248;