7-122985325-G-C

Variant names:

• chr7-122985325-G-C
• rs1308724

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 0.413 in 151,786 control chromosomes in the GnomAD database, including 13,855 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 0.41 (13855 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.561 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: 0.413 AC: 62687 AN: 151668 Hom.: 13840 Cov.: 32

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.413 AC: 62744 AN: 151786 Hom.: 13855 Cov.: 32 AF XY: 0.412 AC XY: 30534 AN XY: 74156

Gnomad4 AFR AF: 0.567

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.320

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.354

Gnomad4 OTH AF: 0.391

Alfa AF: 0.231 Hom.: 492

Bravo AF: 0.410

Asia WGS AF: 0.427 AC: 1485 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.14
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1308724; hg19: chr7-122625379;