rs9856661

chr3-54043229-A-Cchr3-54043229-A-Gchr3-54043229-A-T

Variant summary

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

The ENST00000655075.1(ENSG00000288029):n.1230+4592A>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 0.345 in 152,030 control chromosomes in the GnomAD database, including 13,973 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 0.34 (13973 hom., cov: 32)
• Consequence: ENST00000655075.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.721 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
	ENST00000655075.1	n.1230+4592A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52256 AN: 151912 Hom.: 13922 Cov.: 32

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.345 AC: 52376 AN: 152030 Hom.: 13973 Cov.: 32 AF XY: 0.343 AC XY: 25475 AN XY: 74356

Gnomad4 AFR AF: 0.728

Gnomad4 AMR AF: 0.353

Gnomad4 ASJ AF: 0.197

Gnomad4 EAS AF: 0.486

Gnomad4 SAS AF: 0.345

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.323

Alfa AF: 0.190 Hom.: 5393

Bravo AF: 0.380

Asia WGS AF: 0.433 AC: 1506 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	4.2
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9856661; hg19: chr3-54077256;