7-23180616-T-C

Variant names:

• chr7-23180616-T-C
• rs10254544

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;