rs10447854

Positions:

• chr7-128155752-T-C

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 0.195 in 152,260 control chromosomes in the GnomAD database, including 3,323 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 0.19 (3323 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.259 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: 0.195 AC: 29635 AN: 152142 Hom.: 3319 Cov.: 33

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0721

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.195 AC: 29644 AN: 152260 Hom.: 3323 Cov.: 33 AF XY: 0.186 AC XY: 13827 AN XY: 74458

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.266

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.0717

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.223

Alfa AF: 0.251 Hom.: 9430

Bravo AF: 0.196

Asia WGS AF: 0.0680 AC: 238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.9
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10447854; hg19: chr7-127795804;