chr4-148489167-C-A

Variant names:

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

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:):

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287292	ENST00000661928.1	n.104+43297C>A		intron_variant	Intron 1 of 3
ENSG00000287292	ENST00000669991.1	n.168+43297C>A		intron_variant	Intron 1 of 1
ENSG00000287292	ENST00000817567.1	n.249+46207C>A		intron_variant	Intron 1 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs10519970; hg19: chr4-149410319;