rs6677589

Variant names:

• chr1-58764361-G-A
• rs6677589
• XR_007066136.1:n.3349G>A

Variant summary

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

The XR_007066136.1(LOC105378751):​n.3349G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 152,014 control chromosomes in the GnomAD database, including 27,791 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 0.60 (27791 hom., cov: 32)
• Consequence: LOC105378751 XR_007066136.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.342
• Publications: 12 publications found

Genes affected

LOC105378751 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378751	XR_007066136.1	n.3349G>A		non_coding_transcript_exon_variant	Exon 1 of 3
LOC105378751	XR_007066137.1	n.3349G>A		non_coding_transcript_exon_variant	Exon 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283445	ENST00000636386.1	n.330-1749G>A		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.599 AC: 90965 AN: 151896 Hom.: 27772 Cov.: 32

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.677

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.599 AC: 91024 AN: 152014 Hom.: 27791 Cov.: 32 AF XY: 0.602 AC XY: 44715 AN XY: 74290

African (AFR) AF: 0.473 AC: 19593 AN: 41446

American (AMR) AF: 0.684 AC: 10455 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 2229 AN: 3470

East Asian (EAS) AF: 0.586 AC: 3021 AN: 5158

South Asian (SAS) AF: 0.613 AC: 2959 AN: 4824

European-Finnish (FIN) AF: 0.677 AC: 7145 AN: 10554

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.639 AC: 43426 AN: 67968

Other (OTH) AF: 0.597 AC: 1262 AN: 2114

Alfa AF: 0.626 Hom.: 56242

Bravo AF: 0.594

Asia WGS AF: 0.598 AC: 2081 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	15
DANN	Benign	0.83
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs6677589; hg19: chr1-59230033;