7-122297383-A-T

Variant names:

• chr7-122297383-A-T
• rs538558

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 0.658 in 152,120 control chromosomes in the GnomAD database, including 33,015 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 0.66 (33015 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.582

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.674 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: 0.658 AC: 99965 AN: 152002 Hom.: 32992 Cov.: 33

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.832

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.584

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.789

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.658 AC: 100028 AN: 152120 Hom.: 33015 Cov.: 33 AF XY: 0.659 AC XY: 49040 AN XY: 74380

Gnomad4 AFR AF: 0.623

Gnomad4 AMR AF: 0.610

Gnomad4 ASJ AF: 0.571

Gnomad4 EAS AF: 0.584

Gnomad4 SAS AF: 0.633

Gnomad4 FIN AF: 0.789

Gnomad4 NFE AF: 0.679

Gnomad4 OTH AF: 0.633

Alfa AF: 0.663 Hom.: 4146

Bravo AF: 0.643

Asia WGS AF: 0.586 AC: 2037 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.42
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs538558; hg19: chr7-121937437;