rs1299048

Variant names:

• chr5-162800705-T-A
• rs1299048
• ENST00000646617.1:n.911-4786A>T

Your query was ambiguous. Multiple possible variants found:

• chr5-162800705-T-A
• chr5-162800705-T-G

Variant summary

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

The ENST00000646617.1(ENSG00000254186):​n.911-4786A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.472 in 151,936 control chromosomes in the GnomAD database, including 17,096 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 0.47 (17096 hom., cov: 32)
• Consequence: ENSG00000254186 ENST00000646617.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.292
• Publications: 3 publications found

Genes affected

ENSG00000254186 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000646617.1. 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
	ENSG00000254186	ENST00000646617.1		n.911-4786A>T		intron	N/A
	ENSG00000254186	ENST00000660514.1		n.476-4786A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71626 AN: 151818 Hom.: 17078 Cov.: 32

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.472 AC: 71682 AN: 151936 Hom.: 17096 Cov.: 32 AF XY: 0.477 AC XY: 35393 AN XY: 74254

African (AFR) AF: 0.414 AC: 17151 AN: 41460

American (AMR) AF: 0.537 AC: 8193 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1525 AN: 3468

East Asian (EAS) AF: 0.552 AC: 2843 AN: 5148

South Asian (SAS) AF: 0.587 AC: 2824 AN: 4810

European-Finnish (FIN) AF: 0.488 AC: 5146 AN: 10552

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32575 AN: 67942

Other (OTH) AF: 0.455 AC: 956 AN: 2100

Alfa AF: 0.475 Hom.: 2139

Bravo AF: 0.469

Asia WGS AF: 0.598 AC: 2077 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.8
DANN	Benign	0.38
PhyloP100		0.29

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1299048;

hg19: chr5-162227711;