rs2108178

chr7-41945878-A-G

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 0.243 in 152,102 control chromosomes in the GnomAD database, including 5,355 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 0.24 (5355 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.448

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 (EAS) allele frequency at 95% confidence interval = 0.386 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: 0.243 AC: 36870 AN: 151984 Hom.: 5351 Cov.: 31

Gnomad AFR AF: 0.0776

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.243 AC: 36890 AN: 152102 Hom.: 5355 Cov.: 31 AF XY: 0.242 AC XY: 18005 AN XY: 74344

Gnomad4 AFR AF: 0.0777

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.401

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.277

Alfa AF: 0.292 Hom.: 3477

Bravo AF: 0.231

Asia WGS AF: 0.378 AC: 1317 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	3.6
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2108178; hg19: chr7-41985476;