rs9856661

Variant names:

• chr3-54043229-A-C
• rs9856661
• ENST00000655075.1:n.1230+4592A>C

Your query was ambiguous. Multiple possible variants found:

• chr3-54043229-A-C
• chr3-54043229-A-G
• chr3-54043229-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 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: ENSG00000288029 ENST00000655075.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560

Genes affected

ENSG00000288029 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288029	ENST00000655075.1	n.1230+4592A>C		intron_variant	Intron 2 of 4

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;