7-99960817-C-T

Variant names:

• chr7-99960817-C-T
• rs2107349

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;