chr1-5647756-C-T

Variant names:

• chr1-5647756-C-T
• rs4845812
• ENST00000413887.1:n.155+20385G>A

Variant summary

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

The ENST00000413887.1(ENSG00000289893):​n.155+20385G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 152,040 control chromosomes in the GnomAD database, including 14,055 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 0.41 (14055 hom., cov: 32)
• Consequence: ENSG00000289893 ENST00000413887.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.709
• Publications: 3 publications found

Genes affected

ENSG00000289893 (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 = 0.609 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
ENSG00000289893	ENST00000413887.1	n.155+20385G>A		intron_variant	Intron 1 of 1	5
ENSG00000289893	ENST00000637702.1	n.115+20385G>A		intron_variant	Intron 1 of 2	2
ENSG00000289893	ENST00000727750.1	n.188-68715G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61894 AN: 151920 Hom.: 14013 Cov.: 32

Gnomad AFR AF: 0.614

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.408 AC: 62005 AN: 152040 Hom.: 14055 Cov.: 32 AF XY: 0.406 AC XY: 30132 AN XY: 74288

African (AFR) AF: 0.615 AC: 25490 AN: 41458

American (AMR) AF: 0.364 AC: 5555 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1033 AN: 3470

East Asian (EAS) AF: 0.507 AC: 2619 AN: 5168

South Asian (SAS) AF: 0.312 AC: 1504 AN: 4822

European-Finnish (FIN) AF: 0.285 AC: 3005 AN: 10548

Middle Eastern (MID) AF: 0.229 AC: 67 AN: 292

European-Non Finnish (NFE) AF: 0.317 AC: 21554 AN: 67976

Other (OTH) AF: 0.361 AC: 763 AN: 2114

Alfa AF: 0.347 Hom.: 25478

Bravo AF: 0.425

Asia WGS AF: 0.428 AC: 1489 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	2.6
DANN	Benign	0.92
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs4845812; hg19: chr1-5707816;