rs10486804

Positions:

• chr7-39708306-G-A

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 0.0247 in 152,254 control chromosomes in the GnomAD database, including 88 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 0.025 (88 hom., cov: 33)
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.135 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: 0.0246 AC: 3747 AN: 152136 Hom.: 85 Cov.: 33

Gnomad AFR AF: 0.0258

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0373

Gnomad ASJ AF: 0.0196

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.0539

Gnomad FIN AF: 0.0112

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0126

Gnomad OTH AF: 0.0234

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

GnomAD4 genome AF: 0.0247 AC: 3758 AN: 152254 Hom.: 88 Cov.: 33 AF XY: 0.0256 AC XY: 1905 AN XY: 74440

Gnomad4 AFR AF: 0.0258

Gnomad4 AMR AF: 0.0376

Gnomad4 ASJ AF: 0.0196

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.0543

Gnomad4 FIN AF: 0.0112

Gnomad4 NFE AF: 0.0126

Gnomad4 OTH AF: 0.0232

Alfa AF: 0.0168 Hom.: 48

Bravo AF: 0.0271

Asia WGS AF: 0.0810 AC: 282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.15
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10486804; hg19: chr7-39747905;