rs6427627

Variant names:

• chr1-154386703-T-C
• rs6427627
• ENST00000745817.1:n.212-3325A>G

Variant summary

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

The ENST00000745817.1(ENSG00000297143):​n.212-3325A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 151,974 control chromosomes in the GnomAD database, including 11,410 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 0.38 (11410 hom., cov: 32)
• Consequence: ENSG00000297143 ENST00000745817.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• Publications: 5 publications found

Genes affected

ENSG00000297143 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.402 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
ENSG00000297143	ENST00000745817.1	n.212-3325A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58413 AN: 151858 Hom.: 11389 Cov.: 32

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.385 AC: 58469 AN: 151974 Hom.: 11410 Cov.: 32 AF XY: 0.384 AC XY: 28507 AN XY: 74252

African (AFR) AF: 0.407 AC: 16872 AN: 41446

American (AMR) AF: 0.366 AC: 5582 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1100 AN: 3470

East Asian (EAS) AF: 0.304 AC: 1574 AN: 5174

South Asian (SAS) AF: 0.291 AC: 1399 AN: 4810

European-Finnish (FIN) AF: 0.440 AC: 4642 AN: 10546

Middle Eastern (MID) AF: 0.298 AC: 87 AN: 292

European-Non Finnish (NFE) AF: 0.384 AC: 26120 AN: 67946

Other (OTH) AF: 0.360 AC: 762 AN: 2114

Alfa AF: 0.376 Hom.: 1713

Bravo AF: 0.379

Asia WGS AF: 0.299 AC: 1044 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.56
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs6427627; hg19: chr1-154359179;