rs9959449

chr18-64885416-A-Gchr18-64885416-A-T

Variant summary

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

The ENST00000662570.1(ENSG00000286800):n.307-10332T>C 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 0.446 in 151,970 control chromosomes in the GnomAD database, including 15,426 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 0.45 (15426 hom., cov: 32)
• Consequence: ENST00000662570.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.504 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985178	XR_001753480.1	n.176-25174A>G		intron_variant, non_coding_transcript_variant
LOC101927404	XR_935579.3	n.565-10332T>C		intron_variant, non_coding_transcript_variant
LOC101927404	XR_001753478.1	n.565-10332T>C		intron_variant, non_coding_transcript_variant
LOC101927404	XR_935580.2	n.676-10332T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000662570.1	n.307-10332T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67832 AN: 151852 Hom.: 15419 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.446 AC: 67854 AN: 151970 Hom.: 15426 Cov.: 32 AF XY: 0.439 AC XY: 32638 AN XY: 74282

Gnomad4 AFR AF: 0.392

Gnomad4 AMR AF: 0.416

Gnomad4 ASJ AF: 0.486

Gnomad4 EAS AF: 0.264

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.382

Gnomad4 NFE AF: 0.508

Gnomad4 OTH AF: 0.456

Alfa AF: 0.458 Hom.: 2659

Bravo AF: 0.443

Asia WGS AF: 0.357 AC: 1240 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.8
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9959449; hg19: chr18-62552652;