rs10486784

Variant names:

• chr7-15932146-A-G
• rs10486784

Your query was ambiguous. Multiple possible variants found:

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

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 0.124 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
• Publications: 2 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0307 AC: 1274 AN: 41552

American (AMR) AF: 0.143 AC: 2178 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0885 AC: 307 AN: 3470

East Asian (EAS) AF: 0.348 AC: 1797 AN: 5164

South Asian (SAS) AF: 0.0932 AC: 450 AN: 4828

European-Finnish (FIN) AF: 0.222 AC: 2356 AN: 10600

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10078 AN: 67980

Other (OTH) AF: 0.136 AC: 287 AN: 2108

Alfa AF: 0.137 Hom.: 927

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
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs10486784; hg19: chr7-15971771;