chr7-97104745-A-G

Position:

• chr7-97104745-A-G

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 0.394 in 151,994 control chromosomes in the GnomAD database, including 12,089 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 0.39 (12089 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.473 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: 0.394 AC: 59857 AN: 151876 Hom.: 12064 Cov.: 32

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.394 AC: 59931 AN: 151994 Hom.: 12089 Cov.: 32 AF XY: 0.396 AC XY: 29422 AN XY: 74278

Gnomad4 AFR AF: 0.474

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.489

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.357

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.409

Alfa AF: 0.365 Hom.: 2141

Bravo AF: 0.403

Asia WGS AF: 0.466 AC: 1618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.54
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10246622; hg19: chr7-96734057;