rs2377961

Variant names:

• chr18-9099556-T-C
• rs2377961

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;