rs6897876

Variant names:

• chr5-142308074-T-C
• rs6897876

Your query was ambiguous. Multiple possible variants found:

• chr5-142308074-T-C
• chr5-142308074-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 0.568 in 151,886 control chromosomes in the GnomAD database, including 24,849 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 0.57 (24849 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.635 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: 0.568 AC: 86150 AN: 151766 Hom.: 24837 Cov.: 31

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.568 AC: 86214 AN: 151886 Hom.: 24849 Cov.: 31 AF XY: 0.564 AC XY: 41891 AN XY: 74224

Gnomad4 AFR AF: 0.642

Gnomad4 AMR AF: 0.608

Gnomad4 ASJ AF: 0.642

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.526

Gnomad4 FIN AF: 0.469

Gnomad4 NFE AF: 0.548

Gnomad4 OTH AF: 0.595

Alfa AF: 0.561 Hom.: 6795

Bravo AF: 0.580

Asia WGS AF: 0.430 AC: 1497 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.3
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6897876; hg19: chr5-141687639;