rs10489211

chr1-168343834-A-G

Variant summary

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

The ENST00000636624.1(ENSG00000293102):n.151-24990A>G 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 0.154 in 152,036 control chromosomes in the GnomAD database, including 2,865 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 0.15 (2865 hom., cov: 31)
• Consequence: ENST00000636624.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.898

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000636624.1	n.151-24990A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23378 AN: 151918 Hom.: 2846 Cov.: 31

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.0905

Gnomad ASJ AF: 0.0799

Gnomad EAS AF: 0.00521

Gnomad SAS AF: 0.0909

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0847

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.154 AC: 23442 AN: 152036 Hom.: 2865 Cov.: 31 AF XY: 0.154 AC XY: 11459 AN XY: 74346

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.0902

Gnomad4 ASJ AF: 0.0799

Gnomad4 EAS AF: 0.00522

Gnomad4 SAS AF: 0.0905

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.0847

Gnomad4 OTH AF: 0.137

Alfa AF: 0.0999 Hom.: 605

Bravo AF: 0.160

Asia WGS AF: 0.0700 AC: 246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.91
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10489211; hg19: chr1-168313072;