rs10487416

chr7-120100989-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 0.0514 in 152,190 control chromosomes in the GnomAD database, including 359 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 0.051 (359 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.154

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.12 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: 0.0514 AC: 7814 AN: 152072 Hom.: 358 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0325

Gnomad ASJ AF: 0.0398

Gnomad EAS AF: 0.0317

Gnomad SAS AF: 0.0428

Gnomad FIN AF: 0.0436

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0170

Gnomad OTH AF: 0.0450

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

GnomAD4 genome AF: 0.0514 AC: 7822 AN: 152190 Hom.: 359 Cov.: 32 AF XY: 0.0510 AC XY: 3794 AN XY: 74400

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.0325

Gnomad4 ASJ AF: 0.0398

Gnomad4 EAS AF: 0.0318

Gnomad4 SAS AF: 0.0426

Gnomad4 FIN AF: 0.0436

Gnomad4 NFE AF: 0.0169

Gnomad4 OTH AF: 0.0445

Alfa AF: 0.0435 Hom.: 33

Bravo AF: 0.0527

Asia WGS AF: 0.0410 AC: 143 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	3.8
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10487416; hg19: chr7-119741043;