rs4944804

chr11-72809485-C-Achr11-72809485-C-G

Variant summary

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

The ENST00000624670.2(ENSG00000285693):n.483+956G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,182 control chromosomes in the GnomAD database, including 4,186 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 0.20 (4186 hom., cov: 31)
• Consequence: ENST00000624670.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.410

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984421	XR_007062771.1	n.1435+3148G>T		intron_variant, non_coding_transcript_variant
LOC107984421	XR_001748490.3	n.2482G>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000624670.2	n.483+956G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31149 AN: 152064 Hom.: 4183 Cov.: 31

Gnomad AFR AF: 0.0562

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.0612

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.205 AC: 31153 AN: 152182 Hom.: 4186 Cov.: 31 AF XY: 0.199 AC XY: 14794 AN XY: 74410

Gnomad4 AFR AF: 0.0561

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.0613

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.223

Alfa AF: 0.271 Hom.: 7952

Bravo AF: 0.204

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
Cadd	Benign	4.5
Dann	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4944804; hg19: chr11-72520530;