6-56429484-C-T

Variant names:

• chr6-56429484-C-T
• rs657057
• ENST00000841148.1:n.754+2322G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000841148.1(ENSG00000309441):​n.754+2322G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.55 in 151,868 control chromosomes in the GnomAD database, including 24,782 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 0.55 (24782 hom., cov: 31)
• Consequence: ENSG00000309441 ENST00000841148.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.336
• Publications: 4 publications found

Genes affected

ENSG00000309441 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.711 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
ENSG00000309441	ENST00000841148.1	n.754+2322G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.550 AC: 83490 AN: 151748 Hom.: 24766 Cov.: 31

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.550 AC: 83543 AN: 151868 Hom.: 24782 Cov.: 31 AF XY: 0.557 AC XY: 41379 AN XY: 74226

African (AFR) AF: 0.309 AC: 12803 AN: 41370

American (AMR) AF: 0.618 AC: 9445 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1724 AN: 3468

East Asian (EAS) AF: 0.731 AC: 3759 AN: 5144

South Asian (SAS) AF: 0.590 AC: 2829 AN: 4796

European-Finnish (FIN) AF: 0.742 AC: 7836 AN: 10558

Middle Eastern (MID) AF: 0.541 AC: 158 AN: 292

European-Non Finnish (NFE) AF: 0.638 AC: 43316 AN: 67944

Other (OTH) AF: 0.542 AC: 1144 AN: 2112

Alfa AF: 0.597 Hom.: 14687

Bravo AF: 0.530

Asia WGS AF: 0.641 AC: 2229 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	5.4
DANN	Benign	0.72
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs657057; hg19: chr6-56294282;