rs2027469

Variant names:

• chr1-159697400-G-A
• rs2027469
• ENST00000751816.1:n.108-29127G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-159697400-G-A
• chr1-159697400-G-T

Variant summary

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

The ENST00000751816.1(ENSG00000297913):​n.108-29127G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,134 control chromosomes in the GnomAD database, including 1,667 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 0.13 (1667 hom., cov: 32)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06
• Publications: 6 publications found

Genes affected

ENSG00000297913 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751816.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297913	ENST00000751816.1		n.108-29127G>A		intron	N/A
	ENSG00000297913	ENST00000751817.1		n.110-29127G>A		intron	N/A
	ENSG00000297913	ENST00000751818.1		n.63-29127G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19632 AN: 152016 Hom.: 1665 Cov.: 32

Gnomad AFR AF: 0.0349

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.0345

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.129 AC: 19634 AN: 152134 Hom.: 1667 Cov.: 32 AF XY: 0.128 AC XY: 9497 AN XY: 74368

African (AFR) AF: 0.0348 AC: 1446 AN: 41524

American (AMR) AF: 0.128 AC: 1954 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 480 AN: 3472

East Asian (EAS) AF: 0.0344 AC: 178 AN: 5176

South Asian (SAS) AF: 0.129 AC: 620 AN: 4822

European-Finnish (FIN) AF: 0.167 AC: 1767 AN: 10566

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12563 AN: 67986

Other (OTH) AF: 0.133 AC: 279 AN: 2104

Alfa AF: 0.164 Hom.: 2969

Bravo AF: 0.121

Asia WGS AF: 0.0660 AC: 231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.4
DANN	Benign	0.66
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs2027469; hg19: chr1-159667190;