rs4715555

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

HMGCLL1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HMGCLL1	XM_047418902.1	c.13-41672C>T		intron_variant			XP_047274858.1
HMGCLL1	XM_047418904.1	c.-190+23497C>T		intron_variant			XP_047274860.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.805

Gnomad4 AMR AF: 0.636

Gnomad4 ASJ AF: 0.716

Gnomad4 EAS AF: 0.901

Gnomad4 SAS AF: 0.782

Gnomad4 FIN AF: 0.639

Gnomad4 NFE AF: 0.577

Gnomad4 OTH AF: 0.698

Alfa AF: 0.603 Hom.: 50966

Bravo AF: 0.678

Asia WGS AF: 0.839 AC: 2918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4715555; hg19: chr6-55448610;