rs10214886

Variant names:

• chr6-32889642-T-A
• rs10214886

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 0.142 in 152,212 control chromosomes in the GnomAD database, including 1,836 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 0.14 (1836 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.154

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.226 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: 0.142 AC: 21562 AN: 152094 Hom.: 1832 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.0924

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.142 AC: 21604 AN: 152212 Hom.: 1836 Cov.: 32 AF XY: 0.143 AC XY: 10610 AN XY: 74408

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.0924

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.132

Alfa AF: 0.122 Hom.: 203

Bravo AF: 0.141

Asia WGS AF: 0.171 AC: 591 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.68
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10214886; hg19: chr6-32857419;