rs171866

Positions:

• chr6-115870638-G-A

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 0.72 in 152,130 control chromosomes in the GnomAD database, including 41,350 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 0.72 (41350 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.928 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: 0.720 AC: 109454 AN: 152012 Hom.: 41292 Cov.: 32

Gnomad AFR AF: 0.936

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.717

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

GnomAD4 genome AF: 0.720 AC: 109564 AN: 152130 Hom.: 41350 Cov.: 32 AF XY: 0.711 AC XY: 52850 AN XY: 74342

Gnomad4 AFR AF: 0.936

Gnomad4 AMR AF: 0.554

Gnomad4 ASJ AF: 0.667

Gnomad4 EAS AF: 0.368

Gnomad4 SAS AF: 0.499

Gnomad4 FIN AF: 0.652

Gnomad4 NFE AF: 0.685

Gnomad4 OTH AF: 0.715

Alfa AF: 0.707 Hom.: 4814

Bravo AF: 0.721

Asia WGS AF: 0.501 AC: 1745 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.33
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs171866; hg19: chr6-116191802;