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. The variant received -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
• Publications: 17 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.642 AC: 26566 AN: 41388

American (AMR) AF: 0.608 AC: 9274 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 2225 AN: 3464

East Asian (EAS) AF: 0.297 AC: 1539 AN: 5176

South Asian (SAS) AF: 0.526 AC: 2520 AN: 4792

European-Finnish (FIN) AF: 0.469 AC: 4943 AN: 10532

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.548 AC: 37235 AN: 67956

Other (OTH) AF: 0.595 AC: 1255 AN: 2110

Alfa AF: 0.555 Hom.: 11261

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
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs6897876; hg19: chr5-141687639;