rs10219673

Positions:

• chr12-17487017-T-A
• chr12-17487017-T-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000669683.1(ENSG00000256389):​n.856+6716T>A 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 0.522 in 151,866 control chromosomes in the GnomAD database, including 20,753 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 0.52 (20753 hom., cov: 33)
• Consequence: ENST00000669683.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.46

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.19).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.598 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
	ENST00000669683.1	n.856+6716T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.522 AC: 79190 AN: 151748 Hom.: 20733 Cov.: 33

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.522 AC: 79262 AN: 151866 Hom.: 20753 Cov.: 33 AF XY: 0.525 AC XY: 38979 AN XY: 74226

Gnomad4 AFR AF: 0.515

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.581

Gnomad4 EAS AF: 0.586

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.529

Gnomad4 NFE AF: 0.504

Gnomad4 OTH AF: 0.522

Alfa AF: 0.518 Hom.: 2535

Bravo AF: 0.524

Asia WGS AF: 0.612 AC: 2131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.19
CADD	Benign	22
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10219673; hg19: chr12-17639951;