7-23180616-T-C

Variant names:

• chr7-23180616-T-C
• rs10254544

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 19 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.437 AC: 18118 AN: 41426

American (AMR) AF: 0.306 AC: 4676 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1312 AN: 3470

East Asian (EAS) AF: 0.171 AC: 886 AN: 5192

South Asian (SAS) AF: 0.237 AC: 1141 AN: 4816

European-Finnish (FIN) AF: 0.272 AC: 2878 AN: 10578

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.359 AC: 24419 AN: 68006

Other (OTH) AF: 0.384 AC: 812 AN: 2114

Alfa AF: 0.359 Hom.: 31234

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
PhyloP100		-0.45

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

Other links and lift over

dbSNP: rs10254544; hg19: chr7-23220235;