rs10278040

chr7-99543750-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 0.157 in 152,176 control chromosomes in the GnomAD database, including 3,594 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 0.16 (3594 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.534

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23780 AN: 152058 Hom.: 3579 Cov.: 32

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0424

Gnomad EAS AF: 0.00347

Gnomad SAS AF: 0.0265

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0550

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.157 AC: 23841 AN: 152176 Hom.: 3594 Cov.: 32 AF XY: 0.157 AC XY: 11650 AN XY: 74410

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.0424

Gnomad4 EAS AF: 0.00348

Gnomad4 SAS AF: 0.0263

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.0550

Gnomad4 OTH AF: 0.141

Alfa AF: 0.0894 Hom.: 318

Bravo AF: 0.165

Asia WGS AF: 0.0680 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.9
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: rs10278040; hg19: chr7-99141373;