chr4-11769939-T-A

Variant names:

• chr4-11769939-T-A
• rs10516229
• ENST00000508998.5:n.263-370T>A

Variant summary

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

The ENST00000508998.5(ENSG00000249631):​n.263-370T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0497 in 152,220 control chromosomes in the GnomAD database, including 580 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 0.050 (580 hom., cov: 32)
• Consequence: ENSG00000249631 ENST00000508998.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.50
• Publications: 1 publications found

Genes affected

ENSG00000249631 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986178	NR_188483.1	n.268-370T>A		intron_variant	Intron 2 of 4
LOC107986178	NR_188484.1	n.240-370T>A		intron_variant	Intron 2 of 4
LOC107986178	NR_188485.1	n.157-370T>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000249631	ENST00000508998.5	n.263-370T>A		intron_variant	Intron 2 of 3	3
ENSG00000249631	ENST00000509244.3	n.153-370T>A		intron_variant	Intron 1 of 3	5
ENSG00000249631	ENST00000510095.5	n.142-370T>A		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.0496 AC: 7551 AN: 152102 Hom.: 580 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0268

Gnomad ASJ AF: 0.0150

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00249

Gnomad FIN AF: 0.0000943

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00347

Gnomad OTH AF: 0.0406

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

GnomAD4 genome AF: 0.0497 AC: 7572 AN: 152220 Hom.: 580 Cov.: 32 AF XY: 0.0483 AC XY: 3594 AN XY: 74434

African (AFR) AF: 0.163 AC: 6770 AN: 41518

American (AMR) AF: 0.0268 AC: 409 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0150 AC: 52 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5186

South Asian (SAS) AF: 0.00249 AC: 12 AN: 4824

European-Finnish (FIN) AF: 0.0000943 AC: 1 AN: 10610

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.00347 AC: 236 AN: 68008

Other (OTH) AF: 0.0402 AC: 85 AN: 2116

Alfa AF: 0.0312 Hom.: 41

Bravo AF: 0.0573

Asia WGS AF: 0.0150 AC: 55 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.19
DANN	Benign	0.25
PhyloP100		-2.5
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10516229; hg19: chr4-11771563;