rs1988145

Variant names:

• chr5-92897017-A-C
• rs1988145

Your query was ambiguous. Multiple possible variants found:

• chr5-92897017-A-C
• chr5-92897017-A-G
• chr5-92897017-A-T

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 0.737 in 151,998 control chromosomes in the GnomAD database, including 41,778 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 0.74 (41778 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.847 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: 0.737 AC: 111896 AN: 151880 Hom.: 41726 Cov.: 33

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.768

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.669

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.737 AC: 112006 AN: 151998 Hom.: 41778 Cov.: 33 AF XY: 0.736 AC XY: 54654 AN XY: 74270

Gnomad4 AFR AF: 0.854

Gnomad4 AMR AF: 0.768

Gnomad4 ASJ AF: 0.654

Gnomad4 EAS AF: 0.847

Gnomad4 SAS AF: 0.709

Gnomad4 FIN AF: 0.661

Gnomad4 NFE AF: 0.669

Gnomad4 OTH AF: 0.719

Alfa AF: 0.669 Hom.: 42668

Bravo AF: 0.754

Asia WGS AF: 0.784 AC: 2723 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.1
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1988145; hg19: chr5-92232724; COSMIC: COSV60167871;