rs1322849

Positions:

• chr7-82452223-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 0.31 in 151,912 control chromosomes in the GnomAD database, including 11,542 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 0.31 (11542 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.998

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.674 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: 0.310 AC: 47040 AN: 151794 Hom.: 11508 Cov.: 32

Gnomad AFR AF: 0.680

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.0127

Gnomad SAS AF: 0.0935

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.310 AC: 47124 AN: 151912 Hom.: 11542 Cov.: 32 AF XY: 0.304 AC XY: 22549 AN XY: 74244

Gnomad4 AFR AF: 0.681

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.0128

Gnomad4 SAS AF: 0.0927

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.280

Alfa AF: 0.241 Hom.: 924

Bravo AF: 0.330

Asia WGS AF: 0.0970 AC: 335 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.2
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1322849; hg19: chr7-82081539;