chr4-144749719-T-C

Variant names:

• chr4-144749719-T-C
• rs11944404
• ENST00000649263.1:n.327+314853A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000649263.1(ENSG00000285713):​n.327+314853A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 152,132 control chromosomes in the GnomAD database, including 13,084 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 0.39 (13084 hom., cov: 33)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.934

Genes affected

ENSG00000285713 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900791	XR_007058289.1	n.1304+5438A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285713	ENST00000649263.1	n.327+314853A>G		intron_variant	Intron 4 of 8			ENSP00000497507.1
ENSG00000285783	ENST00000650526.1	n.222+5438A>G		intron_variant	Intron 2 of 14

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59467 AN: 152014 Hom.: 13093 Cov.: 33

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.391 AC: 59456 AN: 152132 Hom.: 13084 Cov.: 33 AF XY: 0.391 AC XY: 29095 AN XY: 74372

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.422

Gnomad4 ASJ AF: 0.409

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.537

Gnomad4 FIN AF: 0.480

Gnomad4 NFE AF: 0.490

Gnomad4 OTH AF: 0.385

Alfa AF: 0.469 Hom.: 33348

Bravo AF: 0.375

Asia WGS AF: 0.315 AC: 1095 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.10
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11944404; hg19: chr4-145670871;