7-97600466-C-T

Position:

• chr7-97600466-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 0.0878 in 152,206 control chromosomes in the GnomAD database, including 799 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 0.088 (799 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.10

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.97600466C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0879 AC: 13365 AN: 152088 Hom.: 799 Cov.: 33

Gnomad AFR AF: 0.0218

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.0916

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0985

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

GnomAD4 genome AF: 0.0878 AC: 13369 AN: 152206 Hom.: 799 Cov.: 33 AF XY: 0.0879 AC XY: 6540 AN XY: 74416

Gnomad4 AFR AF: 0.0217

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.234

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.0916

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.0989

Alfa AF: 0.104 Hom.: 1935

Bravo AF: 0.0878

Asia WGS AF: 0.192 AC: 667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.41
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10486003; hg19: chr7-97229778;