rs10871290

Positions:

• chr16-74438798-C-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, non coding transcript 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: ENST00000669286.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.548

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000669286.1	n.608-982C>T		intron_variant, non_coding_transcript_variant

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;