7-23180616-T-C

Position:

• chr7-23180616-T-C

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 0.359 in 152,084 control chromosomes in the GnomAD database, including 10,201 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 0.36 (10201 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.454

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54598 AN: 151966 Hom.: 10195 Cov.: 33

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.359 AC: 54629 AN: 152084 Hom.: 10201 Cov.: 33 AF XY: 0.352 AC XY: 26163 AN XY: 74362

Gnomad4 AFR AF: 0.437

Gnomad4 AMR AF: 0.306

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.272

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.384

Alfa AF: 0.356 Hom.: 19884

Bravo AF: 0.363

Asia WGS AF: 0.275 AC: 957 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.8
DANN	Benign	0.68

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10254544; hg19: chr7-23220235;