4-144404195-T-C

Variant names:

• chr4-144404195-T-C
• rs951848
• ENST00000649263.1:n.*43+11708A>G

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.*43+11708A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 151,822 control chromosomes in the GnomAD database, including 20,344 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 0.49 (20344 hom., cov: 32)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.211
• Publications: 2 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=-0.64).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377462	XR_939272.3	n.314+11708A>G		intron_variant	Intron 3 of 7
LOC105377462	XR_939273.3	n.240+11708A>G		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285713	ENST00000649263.1	n.*43+11708A>G		intron_variant	Intron 5 of 8			ENSP00000497507.1
ENSG00000285783	ENST00000648340.1	n.214+11708A>G		intron_variant	Intron 2 of 5
ENSG00000285783	ENST00000650526.1	n.298+11708A>G		intron_variant	Intron 3 of 14

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74105 AN: 151704 Hom.: 20334 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.488 AC: 74137 AN: 151822 Hom.: 20344 Cov.: 32 AF XY: 0.494 AC XY: 36674 AN XY: 74194

African (AFR) AF: 0.213 AC: 8820 AN: 41372

American (AMR) AF: 0.518 AC: 7905 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1913 AN: 3470

East Asian (EAS) AF: 0.540 AC: 2766 AN: 5124

South Asian (SAS) AF: 0.636 AC: 3067 AN: 4820

European-Finnish (FIN) AF: 0.647 AC: 6831 AN: 10556

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.604 AC: 40995 AN: 67900

Other (OTH) AF: 0.519 AC: 1095 AN: 2108

Alfa AF: 0.516 Hom.: 2752

Bravo AF: 0.464

Asia WGS AF: 0.509 AC: 1770 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	3.0
DANN	Benign	0.64
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs951848; hg19: chr4-145325347;