rs998124

chr18-45145697-A-Gchr18-45145697-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000660208.1(ENSG00000267101):n.588+4443T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,118 control chromosomes in the GnomAD database, including 1,520 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 0.12 (1520 hom., cov: 31)
• Consequence: ENST00000660208.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.30

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372091	XR_007066349.1	n.216+4443T>C		intron_variant, non_coding_transcript_variant
LOC105372091	XR_935421.3	n.216+4443T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000660208.1	n.588+4443T>C		intron_variant, non_coding_transcript_variant
	ENST00000589845.6	n.438+4443T>C		intron_variant, non_coding_transcript_variant		2
	ENST00000658735.1	n.438+4443T>C		intron_variant, non_coding_transcript_variant
	ENST00000662399.1	n.602+4443T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18714 AN: 152000 Hom.: 1518 Cov.: 31

Gnomad AFR AF: 0.0298

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.0610

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.123 AC: 18707 AN: 152118 Hom.: 1520 Cov.: 31 AF XY: 0.122 AC XY: 9072 AN XY: 74358

Gnomad4 AFR AF: 0.0297

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.0607

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.123

Alfa AF: 0.164 Hom.: 4006

Bravo AF: 0.112

Asia WGS AF: 0.0940 AC: 326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	7.1
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs998124; hg19: chr18-42725662;