rs171866

Variant names:

• chr6-115870638-G-A
• rs171866

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;