rs2108178

Variant names:

• chr7-41945878-A-G
• rs2108178

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 0.243 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0777 AC: 3224 AN: 41510

American (AMR) AF: 0.240 AC: 3665 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1090 AN: 3472

East Asian (EAS) AF: 0.401 AC: 2064 AN: 5150

South Asian (SAS) AF: 0.303 AC: 1456 AN: 4812

European-Finnish (FIN) AF: 0.274 AC: 2900 AN: 10576

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.317 AC: 21577 AN: 67982

Other (OTH) AF: 0.277 AC: 585 AN: 2112

Alfa AF: 0.291 Hom.: 3845

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
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs2108178; hg19: chr7-41985476;