7-99784828-G-C

Position:

• chr7-99784828-G-C

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The variant allele was found at a frequency of 0.0464 in 152,252 control chromosomes in the GnomAD database, including 224 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Likely benign (no stars).

• Frequency: Genomes: 𝑓 0.046 (224 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.322

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 7-99784828-G-C is Benign according to our data. Variant chr7-99784828-G-C is described in Lovd as [Likely_benign].
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0669 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: 0.0464 AC: 7065 AN: 152134 Hom.: 224 Cov.: 32

Gnomad AFR AF: 0.0127

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0395

Gnomad ASJ AF: 0.0490

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0226

Gnomad FIN AF: 0.0781

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0685

Gnomad OTH AF: 0.0549

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

GnomAD4 genome AF: 0.0464 AC: 7064 AN: 152252 Hom.: 224 Cov.: 32 AF XY: 0.0457 AC XY: 3404 AN XY: 74416

Gnomad4 AFR AF: 0.0126

Gnomad4 AMR AF: 0.0395

Gnomad4 ASJ AF: 0.0490

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0228

Gnomad4 FIN AF: 0.0781

Gnomad4 NFE AF: 0.0685

Gnomad4 OTH AF: 0.0543

Alfa AF: 0.0580 Hom.: 42

Bravo AF: 0.0432

Asia WGS AF: 0.0110 AC: 38 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11773597; hg19: chr7-99382451;