rs10486784

Positions:

• chr7-15932146-A-G
• chr7-15932146-A-T

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 0.124 in 152,184 control chromosomes in the GnomAD database, including 1,587 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 0.12 (1587 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18894 AN: 152064 Hom.: 1584 Cov.: 32

Gnomad AFR AF: 0.0307

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.0885

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.0931

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.124 AC: 18902 AN: 152184 Hom.: 1587 Cov.: 32 AF XY: 0.128 AC XY: 9529 AN XY: 74414

Gnomad4 AFR AF: 0.0307

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.0885

Gnomad4 EAS AF: 0.348

Gnomad4 SAS AF: 0.0932

Gnomad4 FIN AF: 0.222

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.136

Alfa AF: 0.137 Hom.: 853

Bravo AF: 0.119

Asia WGS AF: 0.165 AC: 575 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	7.6
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10486784; hg19: chr7-15971771;