rs7072751

Positions:

• chr10-97781347-A-G

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 0.823 in 152,116 control chromosomes in the GnomAD database, including 51,968 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 0.82 (51968 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.967

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 (NFE) allele frequency at 95% confidence interval = 0.876 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: 0.823 AC: 125037 AN: 151998 Hom.: 51933 Cov.: 31

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.894

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.882

Gnomad OTH AF: 0.822

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

GnomAD4 genome AF: 0.823 AC: 125120 AN: 152116 Hom.: 51968 Cov.: 31 AF XY: 0.818 AC XY: 60810 AN XY: 74360

Gnomad4 AFR AF: 0.775

Gnomad4 AMR AF: 0.749

Gnomad4 ASJ AF: 0.829

Gnomad4 EAS AF: 0.521

Gnomad4 SAS AF: 0.783

Gnomad4 FIN AF: 0.894

Gnomad4 NFE AF: 0.882

Gnomad4 OTH AF: 0.822

Alfa AF: 0.855 Hom.: 36854

Bravo AF: 0.806

Asia WGS AF: 0.684 AC: 2374 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.46
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7072751; hg19: chr10-99541104;