chr4-144627781-T-G

Variant names:

• chr4-144627781-T-G
• rs2575570
• ENST00000649263.1:n.328-211803A>C

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.328-211803A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.851 in 152,226 control chromosomes in the GnomAD database, including 55,856 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 0.85 (55856 hom., cov: 33)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.256
• Publications: 7 publications found

Genes affected

ENSG00000285713 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.929 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
ENSG00000285713	ENST00000649263.1	n.328-211803A>C		intron_variant	Intron 4 of 8			ENSP00000497507.1
ENSG00000285783	ENST00000650526.1	n.222+127376A>C		intron_variant	Intron 2 of 14

Frequencies

GnomAD3 genomes AF: 0.851 AC: 129389 AN: 152108 Hom.: 55803 Cov.: 33

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.944

Gnomad AMR AF: 0.848

Gnomad ASJ AF: 0.906

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.899

Gnomad FIN AF: 0.864

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.935

Gnomad OTH AF: 0.867

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

GnomAD4 genome AF: 0.851 AC: 129508 AN: 152226 Hom.: 55856 Cov.: 33 AF XY: 0.846 AC XY: 62962 AN XY: 74426

African (AFR) AF: 0.729 AC: 30233 AN: 41500

American (AMR) AF: 0.848 AC: 12981 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.906 AC: 3147 AN: 3472

East Asian (EAS) AF: 0.594 AC: 3071 AN: 5168

South Asian (SAS) AF: 0.899 AC: 4338 AN: 4826

European-Finnish (FIN) AF: 0.864 AC: 9169 AN: 10608

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.935 AC: 63620 AN: 68030

Other (OTH) AF: 0.865 AC: 1829 AN: 2114

Alfa AF: 0.912 Hom.: 109977

Bravo AF: 0.840

Asia WGS AF: 0.736 AC: 2560 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.37
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs2575570; hg19: chr4-145548933;