rs10519970

Variant names:

• chr4-148489167-C-A
• rs10519970
• ENST00000661928.1:n.104+43297C>A

Your query was ambiguous. Multiple possible variants found:

• chr4-148489167-C-A
• chr4-148489167-C-T

Variant summary

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

The ENST00000661928.1(ENSG00000287292):​n.104+43297C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 151,824 control chromosomes in the GnomAD database, including 24,254 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 0.56 (24254 hom., cov: 31)
• Consequence: ENSG00000287292 ENST00000661928.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104
• Publications: 1 publications found

Genes affected

ENSG00000287292 (HGNC:58892):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.854 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000661928.1. 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
	ENSG00000287292	ENST00000661928.1		n.104+43297C>A		intron	N/A
	ENSG00000287292	ENST00000669991.1		n.168+43297C>A		intron	N/A
	ENSG00000287292	ENST00000817567.1		n.249+46207C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84742 AN: 151708 Hom.: 24227 Cov.: 31

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.875

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.559 AC: 84819 AN: 151824 Hom.: 24254 Cov.: 31 AF XY: 0.571 AC XY: 42360 AN XY: 74218

African (AFR) AF: 0.496 AC: 20512 AN: 41392

American (AMR) AF: 0.641 AC: 9776 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.521 AC: 1806 AN: 3466

East Asian (EAS) AF: 0.875 AC: 4527 AN: 5172

South Asian (SAS) AF: 0.645 AC: 3110 AN: 4824

European-Finnish (FIN) AF: 0.684 AC: 7202 AN: 10528

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.531 AC: 36064 AN: 67882

Other (OTH) AF: 0.544 AC: 1152 AN: 2116

Alfa AF: 0.413 Hom.: 1226

Bravo AF: 0.555

Asia WGS AF: 0.778 AC: 2701 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.0
DANN	Benign	0.28
PhyloP100		-0.10

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: rs10519970;

hg19: chr4-149410319;