rs10754012

Positions:

• chr1-192523765-A-G
• chr1-192523765-A-T

Variant summary

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

The ENST00000642657.1(ENSG00000236069):​n.717+5859A>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 0.834 in 152,172 control chromosomes in the GnomAD database, including 53,307 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 0.83 (53307 hom., cov: 32)
• Consequence: ENST00000642657.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.916

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105371664	XR_002958418.2	n.358-5802T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000642657.1	n.717+5859A>G		intron_variant, non_coding_transcript_variant
	ENST00000644134.1	n.596-31796T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.834 AC: 126755 AN: 152054 Hom.: 53248 Cov.: 32

Gnomad AFR AF: 0.946

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.884

Gnomad FIN AF: 0.784

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.782

Gnomad OTH AF: 0.824

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

GnomAD4 genome AF: 0.834 AC: 126871 AN: 152172 Hom.: 53307 Cov.: 32 AF XY: 0.835 AC XY: 62116 AN XY: 74386

Gnomad4 AFR AF: 0.946

Gnomad4 AMR AF: 0.801

Gnomad4 ASJ AF: 0.814

Gnomad4 EAS AF: 0.793

Gnomad4 SAS AF: 0.884

Gnomad4 FIN AF: 0.784

Gnomad4 NFE AF: 0.782

Gnomad4 OTH AF: 0.820

Alfa AF: 0.798 Hom.: 8657

Bravo AF: 0.839

Asia WGS AF: 0.846 AC: 2944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.44
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10754012; hg19: chr1-192492895;