rs9480303

Positions:

• chr6-156299172-T-C

Variant summary

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

The ENST00000663591.1(ENSG00000287092):​n.225-4418A>G 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 0.448 in 151,940 control chromosomes in the GnomAD database, including 15,800 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 (15800 hom., cov: 32)
• Consequence: ENST00000663591.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.71

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.534 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
	ENST00000663591.1	n.225-4418A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.448 AC: 68069 AN: 151822 Hom.: 15780 Cov.: 32

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.448 AC: 68140 AN: 151940 Hom.: 15800 Cov.: 32 AF XY: 0.452 AC XY: 33565 AN XY: 74256

Gnomad4 AFR AF: 0.540

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.496

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.423

Alfa AF: 0.441 Hom.: 3468

Bravo AF: 0.434

Asia WGS AF: 0.531 AC: 1842 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.54
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9480303; hg19: chr6-156620306;