rs10493011

Positions:

• chr1-22149323-G-A
• chr1-22149323-G-C

Variant summary

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

The ENST00000648968.1(ENSG00000285873):​n.56-5580G>A 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 0.0479 in 152,168 control chromosomes in the GnomAD database, including 292 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 0.048 (292 hom., cov: 32)
• Consequence: ENST00000648968.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376845	XR_947050.1	n.54-5580G>A		intron_variant, non_coding_transcript_variant
LOC105376845	XR_947051.3	n.143-5580G>A		intron_variant, non_coding_transcript_variant
LOC105376845	XR_947056.2	n.143-5580G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000648968.1	n.56-5580G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0479 AC: 7289 AN: 152050 Hom.: 294 Cov.: 32

Gnomad AFR AF: 0.0830

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0891

Gnomad ASJ AF: 0.0452

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.0342

Gnomad FIN AF: 0.0609

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0119

Gnomad OTH AF: 0.0464

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

GnomAD4 genome AF: 0.0479 AC: 7291 AN: 152168 Hom.: 292 Cov.: 32 AF XY: 0.0502 AC XY: 3733 AN XY: 74392

Gnomad4 AFR AF: 0.0828

Gnomad4 AMR AF: 0.0892

Gnomad4 ASJ AF: 0.0452

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.0342

Gnomad4 FIN AF: 0.0609

Gnomad4 NFE AF: 0.0119

Gnomad4 OTH AF: 0.0464

Alfa AF: 0.0277 Hom.: 29

Bravo AF: 0.0508

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	-0.96
CADD	Benign	2.3
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10493011; hg19: chr1-22475816;