rs10207319

Variant names:

• chr2-47970910-A-T
• rs10207319
• ENST00000447571.5:n.442-22501T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000447571.5(ENSG00000230773):​n.442-22501T>A variant causes a intron 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: ENSG00000230773 ENST00000447571.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.182
• Publications: 3 publications found

Genes affected

ENSG00000230773 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000447571.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000230773	ENST00000447571.5	TSL:1	n.442-22501T>A		intron	N/A
	ENSG00000230773	ENST00000587616.1	TSL:5	n.944-8334T>A		intron	N/A
	ENSG00000230773	ENST00000649883.1		n.403-22501T>A		intron	N/A

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

African (AFR) AF: 0.111 AC: 4609 AN: 41530

American (AMR) AF: 0.293 AC: 4480 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1092 AN: 3470

East Asian (EAS) AF: 0.0659 AC: 342 AN: 5186

South Asian (SAS) AF: 0.299 AC: 1438 AN: 4814

European-Finnish (FIN) AF: 0.418 AC: 4416 AN: 10556

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.377 AC: 25649 AN: 67964

Other (OTH) AF: 0.294 AC: 622 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.9
DANN	Benign	0.78
PhyloP100		0.18

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10207319;

hg19: chr2-48198049;