rs6872786

chr5-105644654-T-C

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 0.643 in 151,924 control chromosomes in the GnomAD database, including 31,971 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 0.64 (31971 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.376

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97551 AN: 151806 Hom.: 31920 Cov.: 32

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.669

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.643 AC: 97665 AN: 151924 Hom.: 31971 Cov.: 32 AF XY: 0.637 AC XY: 47284 AN XY: 74252

Gnomad4 AFR AF: 0.713

Gnomad4 AMR AF: 0.697

Gnomad4 ASJ AF: 0.633

Gnomad4 EAS AF: 0.318

Gnomad4 SAS AF: 0.669

Gnomad4 FIN AF: 0.513

Gnomad4 NFE AF: 0.632

Gnomad4 OTH AF: 0.656

Alfa AF: 0.639 Hom.: 59815

Bravo AF: 0.655

Asia WGS AF: 0.532 AC: 1851 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	4.5
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6872786; hg19: chr5-104980355;