rs6754829

Variant names:

• chr2-122801913-T-C
• rs6754829
• ENST00000657880.2:n.825-21841T>C

Variant summary

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

The ENST00000657880.2(ENSG00000286481):​n.825-21841T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0177 in 152,270 control chromosomes in the GnomAD database, including 39 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 0.018 (39 hom., cov: 32)
• Consequence: ENSG00000286481 ENST00000657880.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.46
• Publications: 1 publications found

Genes affected

ENSG00000286481 (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 (SAS) allele frequency at 95% confidence interval = 0.067 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373594	XR_923288.1	n.1553-416A>G		intron_variant	Intron 3 of 3
LOC105373594	XR_923289.3	n.1553-1697A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286481	ENST00000657880.2	n.825-21841T>C		intron_variant	Intron 4 of 8
ENSG00000286481	ENST00000687364.1	n.84-21841T>C		intron_variant	Intron 1 of 5
ENSG00000286481	ENST00000770504.1	n.365-21841T>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.0176 AC: 2677 AN: 152152 Hom.: 41 Cov.: 32

Gnomad AFR AF: 0.0381

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0101

Gnomad ASJ AF: 0.0799

Gnomad EAS AF: 0.00347

Gnomad SAS AF: 0.0736

Gnomad FIN AF: 0.0000942

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.00350

Gnomad OTH AF: 0.0191

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

GnomAD4 genome AF: 0.0177 AC: 2690 AN: 152270 Hom.: 39 Cov.: 32 AF XY: 0.0184 AC XY: 1367 AN XY: 74460

African (AFR) AF: 0.0383 AC: 1592 AN: 41540

American (AMR) AF: 0.0101 AC: 155 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0799 AC: 277 AN: 3466

East Asian (EAS) AF: 0.00367 AC: 19 AN: 5172

South Asian (SAS) AF: 0.0733 AC: 354 AN: 4832

European-Finnish (FIN) AF: 0.0000942 AC: 1 AN: 10620

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.00350 AC: 238 AN: 68026

Other (OTH) AF: 0.0194 AC: 41 AN: 2114

Alfa AF: 0.0114 Hom.: 3

Bravo AF: 0.0169

Asia WGS AF: 0.0460 AC: 161 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	0.030
DANN	Benign	0.44
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs6754829; hg19: chr2-123559489;