rs1556547

Variant names:

• chr6-10270144-G-A
• rs1556547
• ENST00000829457.1:n.353-1077C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-10270144-G-A
• chr6-10270144-G-T

Variant summary

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

The ENST00000829457.1(ENSG00000307859):​n.353-1077C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.542 in 151,542 control chromosomes in the GnomAD database, including 22,676 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 0.54 (22676 hom., cov: 32)
• Consequence: ENSG00000307859 ENST00000829457.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150
• Publications: 3 publications found

Genes affected

ENSG00000307859 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.62 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
ENSG00000307859	ENST00000829457.1	n.353-1077C>T		intron_variant	Intron 4 of 5
ENSG00000307859	ENST00000829458.1	n.448-1077C>T		intron_variant	Intron 5 of 6
ENSG00000307877	ENST00000829572.1	n.55+1779G>A		intron_variant	Intron 1 of 3
ENSG00000307877	ENST00000829573.1	n.63+1779G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.542 AC: 82107 AN: 151426 Hom.: 22650 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.858

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.542 AC: 82180 AN: 151542 Hom.: 22676 Cov.: 32 AF XY: 0.537 AC XY: 39731 AN XY: 74034

African (AFR) AF: 0.447 AC: 18458 AN: 41284

American (AMR) AF: 0.630 AC: 9589 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1987 AN: 3460

East Asian (EAS) AF: 0.274 AC: 1413 AN: 5150

South Asian (SAS) AF: 0.527 AC: 2531 AN: 4806

European-Finnish (FIN) AF: 0.545 AC: 5721 AN: 10490

Middle Eastern (MID) AF: 0.589 AC: 172 AN: 292

European-Non Finnish (NFE) AF: 0.594 AC: 40299 AN: 67832

Other (OTH) AF: 0.586 AC: 1234 AN: 2106

Alfa AF: 0.581 Hom.: 81670

Bravo AF: 0.551

Asia WGS AF: 0.485 AC: 1686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	10
DANN	Benign	0.76
PhyloP100		-0.015

Splicing

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

Other links and lift over

dbSNP: rs1556547; hg19: chr6-10270377;