rs10499970

chr7-109463692-A-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 0.0599 in 152,294 control chromosomes in the GnomAD database, including 304 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 0.060 (304 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.575

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.093 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: 0.0600 AC: 9125 AN: 152176 Hom.: 307 Cov.: 33

Gnomad AFR AF: 0.0957

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0465

Gnomad ASJ AF: 0.0541

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0399

Gnomad FIN AF: 0.0384

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0507

Gnomad OTH AF: 0.0693

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

GnomAD4 genome AF: 0.0599 AC: 9123 AN: 152294 Hom.: 304 Cov.: 33 AF XY: 0.0586 AC XY: 4366 AN XY: 74464

Gnomad4 AFR AF: 0.0955

Gnomad4 AMR AF: 0.0464

Gnomad4 ASJ AF: 0.0541

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0391

Gnomad4 FIN AF: 0.0384

Gnomad4 NFE AF: 0.0507

Gnomad4 OTH AF: 0.0686

Alfa AF: 0.0524 Hom.: 127

Bravo AF: 0.0627

Asia WGS AF: 0.0160 AC: 54 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
Cadd	Benign	1.4
Dann	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10499970; hg19: chr7-109103749;