rs6871240

Variant names:

• chr5-107794718-G-A
• rs6871240

Your query was ambiguous. Multiple possible variants found:

• chr5-107794718-G-A
• chr5-107794718-G-T

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 0.279 in 152,092 control chromosomes in the GnomAD database, including 7,117 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 0.28 (7117 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.243
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42491 AN: 151974 Hom.: 7117 Cov.: 32

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.279 AC: 42500 AN: 152092 Hom.: 7117 Cov.: 32 AF XY: 0.274 AC XY: 20379 AN XY: 74336

African (AFR) AF: 0.115 AC: 4774 AN: 41514

American (AMR) AF: 0.267 AC: 4088 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1686 AN: 3468

East Asian (EAS) AF: 0.136 AC: 705 AN: 5166

South Asian (SAS) AF: 0.193 AC: 931 AN: 4818

European-Finnish (FIN) AF: 0.333 AC: 3517 AN: 10558

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.377 AC: 25638 AN: 67972

Other (OTH) AF: 0.301 AC: 633 AN: 2106

Alfa AF: 0.287 Hom.: 2541

Bravo AF: 0.269

Asia WGS AF: 0.187 AC: 653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.0
DANN	Benign	0.74
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs6871240; hg19: chr5-107130419;