rs549471

Variant names:

• chr1-160735829-T-A
• rs549471
• ENST00000792523.1:n.73-3212A>T

Your query was ambiguous. Multiple possible variants found:

• chr1-160735829-T-A
• chr1-160735829-T-C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000792523.1(ENSG00000303180):​n.73-3212A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000414 in 145,072 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000041 (0 hom., cov: 23)
• Consequence: ENSG00000303180 ENST00000792523.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• Publications: 6 publications found

Genes affected

ENSG00000303180 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904440	XR_007066687.1	n.78-1576A>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303180	ENST00000792523.1	n.73-3212A>T		intron_variant	Intron 1 of 1
ENSG00000303180	ENST00000792524.1	n.393-3212A>T		intron_variant	Intron 2 of 2
ENSG00000303180	ENST00000792525.1	n.658-3212A>T		intron_variant	Intron 3 of 3
ENSG00000303202	ENST00000792685.1	n.157-1576A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0000414 AC: 6 AN: 144952 Hom.: 0 Cov.: 23

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00129

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.0000414 AC: 6 AN: 145072 Hom.: 0 Cov.: 23 AF XY: 0.0000574 AC XY: 4 AN XY: 69722

African (AFR) AF: 0.00 AC: 0 AN: 39666

American (AMR) AF: 0.00 AC: 0 AN: 14032

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3438

East Asian (EAS) AF: 0.00 AC: 0 AN: 4734

South Asian (SAS) AF: 0.00130 AC: 6 AN: 4630

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8116

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67234

Other (OTH) AF: 0.00 AC: 0 AN: 2032

Alfa AF: 0.00 Hom.: 94221

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.98
DANN	Benign	0.49
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs549471; hg19: chr1-160705619;