rs10055544

Variant names:

• chr5-92222904-G-A
• rs10055544
• ENST00000502934.1:n.172+18220G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-92222904-G-A
• chr5-92222904-G-T

Variant summary

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

The ENST00000502934.1(ENSG00000250049):​n.172+18220G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0611 in 152,160 control chromosomes in the GnomAD database, including 289 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 0.061 (289 hom., cov: 32)
• Consequence: ENSG00000250049 ENST00000502934.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.190
• Publications: 4 publications found

Genes affected

ENSG00000250049 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.068 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000502934.1. 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
	ENSG00000250049	ENST00000502934.1	TSL:2	n.172+18220G>A		intron	N/A
	ENSG00000250049	ENST00000507217.5	TSL:4	n.304+18220G>A		intron	N/A
	ENSG00000250049	ENST00000850170.1		n.281+18220G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0612 AC: 9298 AN: 152042 Hom.: 291 Cov.: 32

Gnomad AFR AF: 0.0481

Gnomad AMI AF: 0.0989

Gnomad AMR AF: 0.0522

Gnomad ASJ AF: 0.0919

Gnomad EAS AF: 0.00716

Gnomad SAS AF: 0.0716

Gnomad FIN AF: 0.0739

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0697

Gnomad OTH AF: 0.0761

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

GnomAD4 genome AF: 0.0611 AC: 9295 AN: 152160 Hom.: 289 Cov.: 32 AF XY: 0.0606 AC XY: 4505 AN XY: 74396

African (AFR) AF: 0.0480 AC: 1992 AN: 41510

American (AMR) AF: 0.0522 AC: 798 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0919 AC: 319 AN: 3470

East Asian (EAS) AF: 0.00718 AC: 37 AN: 5154

South Asian (SAS) AF: 0.0712 AC: 344 AN: 4830

European-Finnish (FIN) AF: 0.0739 AC: 784 AN: 10602

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0697 AC: 4738 AN: 67978

Other (OTH) AF: 0.0753 AC: 159 AN: 2112

Alfa AF: 0.0657 Hom.: 612

Bravo AF: 0.0575

Asia WGS AF: 0.0410 AC: 142 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.2
DANN	Benign	0.34
PhyloP100		0.19
Mutation Taster		=100/0	polymorphism

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: rs10055544;

hg19: chr5-91518721;