7-107839870-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 0.674 in 152,174 control chromosomes in the GnomAD database, including 35,339 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 0.67 (35339 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

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 (EAS) allele frequency at 95% confidence interval = 0.849 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: 0.674 AC: 102483 AN: 152056 Hom.: 35291 Cov.: 32

Gnomad AFR AF: 0.805

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.640

Gnomad NFE AF: 0.600

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.674 AC: 102586 AN: 152174 Hom.: 35339 Cov.: 32 AF XY: 0.676 AC XY: 50277 AN XY: 74384

Gnomad4 AFR AF: 0.806

Gnomad4 AMR AF: 0.659

Gnomad4 ASJ AF: 0.626

Gnomad4 EAS AF: 0.871

Gnomad4 SAS AF: 0.579

Gnomad4 FIN AF: 0.625

Gnomad4 NFE AF: 0.600

Gnomad4 OTH AF: 0.666

Alfa AF: 0.579 Hom.: 9371

Bravo AF: 0.684

Asia WGS AF: 0.748 AC: 2603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.1
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4380874; hg19: chr7-107480315;