rs4715555

Variant names:

• chr6-55583812-G-A
• rs4715555
• XM_047418902.1:c.13-41672C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-55583812-G-A
• chr6-55583812-G-C
• chr6-55583812-G-T

Variant summary

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

The XM_047418902.1(HMGCLL1):​c.13-41672C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.672 in 151,972 control chromosomes in the GnomAD database, including 35,281 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 0.67 (35281 hom., cov: 32)
• Consequence: HMGCLL1 XM_047418902.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.195
• Publications: 11 publications found

Genes affected

HMGCLL1 (HGNC:21359): (3-hydroxy-3-methylglutaryl-CoA lyase like 1) Enables hydroxymethylglutaryl-CoA lyase activity. Involved in ketone body biosynthetic process. Located in several cellular components, including cytosol; endoplasmic reticulum; and perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.88 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.672 AC: 102091 AN: 151854 Hom.: 35235 Cov.: 32

Gnomad AFR AF: 0.805

Gnomad AMI AF: 0.624

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.716

Gnomad EAS AF: 0.901

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.672 AC: 102197 AN: 151972 Hom.: 35281 Cov.: 32 AF XY: 0.680 AC XY: 50498 AN XY: 74300

African (AFR) AF: 0.805 AC: 33401 AN: 41482

American (AMR) AF: 0.636 AC: 9690 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.716 AC: 2478 AN: 3462

East Asian (EAS) AF: 0.901 AC: 4654 AN: 5164

South Asian (SAS) AF: 0.782 AC: 3766 AN: 4818

European-Finnish (FIN) AF: 0.639 AC: 6759 AN: 10572

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.577 AC: 39190 AN: 67928

Other (OTH) AF: 0.698 AC: 1469 AN: 2106

Alfa AF: 0.611 Hom.: 119063

Bravo AF: 0.678

Asia WGS AF: 0.839 AC: 2918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.55
DANN	Benign	0.57
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs4715555; hg19: chr6-55448610;