rs1010003

Variant names:

• chr18-965989-T-C
• rs1010003
• ENST00000606879.1:n.141-2727A>G

Variant summary

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

The ENST00000606879.1(ENSG00000272461):​n.141-2727A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,202 control chromosomes in the GnomAD database, including 1,894 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 0.14 (1894 hom., cov: 33)
• Consequence: ENSG00000272461 ENST00000606879.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.433
• Publications: 2 publications found

Genes affected

ENSG00000272461 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000606879.1. 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
	ENSG00000272461	ENST00000606879.1	TSL:3	n.141-2727A>G		intron	N/A
	ENSG00000298195	ENST00000753835.1		n.151+14711T>C		intron	N/A
	ENSG00000272461	ENST00000754058.1		n.136-3034A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21215 AN: 152084 Hom.: 1893 Cov.: 33

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.0675

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.0954

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.139 AC: 21218 AN: 152202 Hom.: 1894 Cov.: 33 AF XY: 0.136 AC XY: 10152 AN XY: 74434

African (AFR) AF: 0.251 AC: 10408 AN: 41508

American (AMR) AF: 0.104 AC: 1587 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 420 AN: 3470

East Asian (EAS) AF: 0.108 AC: 559 AN: 5178

South Asian (SAS) AF: 0.110 AC: 530 AN: 4816

European-Finnish (FIN) AF: 0.0675 AC: 716 AN: 10600

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.0954 AC: 6489 AN: 68012

Other (OTH) AF: 0.140 AC: 297 AN: 2116

Alfa AF: 0.114 Hom.: 1619

Bravo AF: 0.148

Asia WGS AF: 0.142 AC: 493 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.3
DANN	Benign	0.48
PhyloP100		-0.43

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: rs1010003;

hg19: chr18-965990;