rs10207319

chr2-47970910-A-T

Variant summary

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

The ENST00000447571.5(ENSG00000230773):n.442-22501T>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 0.283 in 152,118 control chromosomes in the GnomAD database, including 7,366 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 0.28 (7366 hom., cov: 32)
• Consequence: ENST00000447571.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.182

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 = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374591	XR_001739454.2	n.455+25806T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000447571.5	n.442-22501T>A		intron_variant, non_coding_transcript_variant		1
	ENST00000651429.1	n.417-20647T>A		intron_variant, non_coding_transcript_variant
	ENST00000587616.1	n.944-8334T>A		intron_variant, non_coding_transcript_variant		5
	ENST00000649883.1	n.403-22501T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.283 AC: 43073 AN: 152000 Hom.: 7364 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.0660

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.283 AC: 43081 AN: 152118 Hom.: 7366 Cov.: 32 AF XY: 0.282 AC XY: 20993 AN XY: 74340

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.0659

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.418

Gnomad4 NFE AF: 0.377

Gnomad4 OTH AF: 0.294

Alfa AF: 0.336 Hom.: 1300

Bravo AF: 0.263

Asia WGS AF: 0.173 AC: 601 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	5.9
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10207319; hg19: chr2-48198049;