rs2377961

Positions:

• chr18-9099556-T-C
• chr18-9099556-T-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 0.34 in 152,054 control chromosomes in the GnomAD database, including 9,087 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 0.34 (9087 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.418 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: 0.340 AC: 51692 AN: 151936 Hom.: 9081 Cov.: 32

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.340 AC: 51720 AN: 152054 Hom.: 9087 Cov.: 32 AF XY: 0.338 AC XY: 25087 AN XY: 74320

Gnomad4 AFR AF: 0.354

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.459

Gnomad4 EAS AF: 0.320

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.373

Alfa AF: 0.333 Hom.: 13331

Bravo AF: 0.357

Asia WGS AF: 0.298 AC: 1034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.9
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2377961; hg19: chr18-9099554;