5-57658989-G-C

Variant names:

• chr5-57658989-G-C
• rs230827
• ENST00000661344.3:n.212-6262G>C

Variant summary

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

The NR_104668.1(LOC101928505):​n.101-6262G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 151,896 control chromosomes in the GnomAD database, including 11,779 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 (11779 hom., cov: 32)
• Consequence: LOC101928505 NR_104668.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 0 publications found

Genes affected

ENSG00000287709 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_104668.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC101928505	NR_104668.1		n.101-6262G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287709	ENST00000661344.3		n.212-6262G>C		intron	N/A
	ENSG00000287709	ENST00000685494.1		n.105-6262G>C		intron	N/A
	ENSG00000287709	ENST00000688166.1		n.89-6262G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52160 AN: 151778 Hom.: 11736 Cov.: 32

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.344 AC: 52270 AN: 151896 Hom.: 11779 Cov.: 32 AF XY: 0.340 AC XY: 25283 AN XY: 74256

African (AFR) AF: 0.645 AC: 26718 AN: 41402

American (AMR) AF: 0.269 AC: 4109 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 728 AN: 3464

East Asian (EAS) AF: 0.311 AC: 1606 AN: 5158

South Asian (SAS) AF: 0.153 AC: 736 AN: 4804

European-Finnish (FIN) AF: 0.258 AC: 2728 AN: 10586

Middle Eastern (MID) AF: 0.233 AC: 68 AN: 292

European-Non Finnish (NFE) AF: 0.217 AC: 14737 AN: 67920

Other (OTH) AF: 0.334 AC: 705 AN: 2110

Alfa AF: 0.276 Hom.: 894

Bravo AF: 0.361

Asia WGS AF: 0.297 AC: 1032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	6.6
DANN	Benign	0.84
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs230827; hg19: chr5-56954816;