7-123208562-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 0.335 in 151,436 control chromosomes in the GnomAD database, including 9,168 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 0.33 (9168 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.460

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 (SAS) allele frequency at 95% confidence interval = 0.385 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: 0.335 AC: 50667 AN: 151318 Hom.: 9164 Cov.: 31

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.335 AC: 50669 AN: 151436 Hom.: 9168 Cov.: 31 AF XY: 0.340 AC XY: 25182 AN XY: 73992

Gnomad4 AFR AF: 0.184

Gnomad4 AMR AF: 0.387

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.384

Gnomad4 OTH AF: 0.324

Alfa AF: 0.264 Hom.: 723

Bravo AF: 0.323

Asia WGS AF: 0.340 AC: 1181 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	3.4
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10487974; hg19: chr7-122848616;