rs10871290

Variant names:

• chr16-74438798-C-T
• rs10871290
• ENST00000669286.1:n.608-982C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000669286.1(ENSG00000261170):​n.608-982C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.616 in 152,026 control chromosomes in the GnomAD database, including 29,206 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 0.62 (29206 hom., cov: 32)
• Consequence: ENSG00000261170 ENST00000669286.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.548

Genes affected

ENSG00000261170 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.731 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
ENSG00000261170	ENST00000669286.1	n.608-982C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.616 AC: 93579 AN: 151908 Hom.: 29186 Cov.: 32

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.616 AC: 93652 AN: 152026 Hom.: 29206 Cov.: 32 AF XY: 0.620 AC XY: 46084 AN XY: 74282

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.712

Gnomad4 ASJ AF: 0.625

Gnomad4 EAS AF: 0.619

Gnomad4 SAS AF: 0.752

Gnomad4 FIN AF: 0.629

Gnomad4 NFE AF: 0.640

Gnomad4 OTH AF: 0.611

Alfa AF: 0.639 Hom.: 35018

Bravo AF: 0.617

Asia WGS AF: 0.660 AC: 2295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.4
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10871290; hg19: chr16-74472696; COSMIC: COSV73722799;