7-99960817-C-T

Position:

• chr7-99960817-C-T

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 0.975 in 151,948 control chromosomes in the GnomAD database, including 72,161 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 0.97 (72161 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 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: 0.975 AC: 147969 AN: 151830 Hom.: 72105 Cov.: 29

Gnomad AFR AF: 0.980

Gnomad AMI AF: 0.998

Gnomad AMR AF: 0.968

Gnomad ASJ AF: 0.974

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.966

Gnomad FIN AF: 0.984

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.970

Gnomad OTH AF: 0.966

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

GnomAD4 genome AF: 0.975 AC: 148085 AN: 151948 Hom.: 72161 Cov.: 29 AF XY: 0.975 AC XY: 72417 AN XY: 74254

Gnomad4 AFR AF: 0.980

Gnomad4 AMR AF: 0.968

Gnomad4 ASJ AF: 0.974

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.966

Gnomad4 FIN AF: 0.984

Gnomad4 NFE AF: 0.970

Gnomad4 OTH AF: 0.966

Alfa AF: 0.970 Hom.: 38879

Bravo AF: 0.974

Asia WGS AF: 0.973 AC: 3385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
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: rs2107349; hg19: chr7-99558440;