rs1844549

Variant names:

• chr10-18714366-C-G
• rs1844549
• ENST00000654305.2:n.103+4005C>G

Variant summary

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

The ENST00000654305.2(ENSG00000234244):​n.103+4005C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 151,968 control chromosomes in the GnomAD database, including 2,381 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 0.17 (2381 hom., cov: 32)
• Consequence: ENSG00000234244 ENST00000654305.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480
• Publications: 1 publications found

Genes affected

ENSG00000234244 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654305.2. 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
	ENSG00000234244	ENST00000654305.2		n.103+4005C>G		intron	N/A
	ENSG00000234244	ENST00000654415.1		n.78+4005C>G		intron	N/A
	ENSG00000234244	ENST00000723466.1		n.53+4005C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.171 AC: 25926 AN: 151850 Hom.: 2379 Cov.: 32

Gnomad AFR AF: 0.0999

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.171 AC: 25937 AN: 151968 Hom.: 2381 Cov.: 32 AF XY: 0.170 AC XY: 12618 AN XY: 74298

African (AFR) AF: 0.0997 AC: 4133 AN: 41446

American (AMR) AF: 0.166 AC: 2539 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 731 AN: 3466

East Asian (EAS) AF: 0.211 AC: 1089 AN: 5152

South Asian (SAS) AF: 0.126 AC: 606 AN: 4798

European-Finnish (FIN) AF: 0.204 AC: 2148 AN: 10550

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14062 AN: 67984

Other (OTH) AF: 0.164 AC: 346 AN: 2104

Alfa AF: 0.193 Hom.: 375

Bravo AF: 0.165

Asia WGS AF: 0.175 AC: 607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.70
PhyloP100		-0.048

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: rs1844549;

hg19: chr10-19003295;