7-23554431-C-T

Position:

• chr7-23554431-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 0.528 in 148,106 control chromosomes in the GnomAD database, including 20,938 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 0.53 (20938 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.619 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: 0.528 AC: 78132 AN: 147994 Hom.: 20907 Cov.: 25

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.550

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.528 AC: 78220 AN: 148106 Hom.: 20938 Cov.: 25 AF XY: 0.521 AC XY: 37458 AN XY: 71930

Gnomad4 AFR AF: 0.625

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.406

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.513

Gnomad4 OTH AF: 0.542

Alfa AF: 0.496 Hom.: 2536

Bravo AF: 0.536

Asia WGS AF: 0.396 AC: 1381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.18
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6949019; hg19: chr7-23594050;