4-11628425-T-C

Variant names:

• chr4-11628425-T-C
• rs6448799
• ENST00000510095.5:n.98+2614T>C

Variant summary

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

The ENST00000510095.5(ENSG00000249631):​n.98+2614T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.731 in 152,114 control chromosomes in the GnomAD database, including 41,881 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 0.73 (41881 hom., cov: 33)
• Consequence: ENSG00000249631 ENST00000510095.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62
• Publications: 15 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986178	NR_188483.1	n.267+76471T>C		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000249631	ENST00000510095.5	n.98+2614T>C		intron_variant	Intron 1 of 3	3
ENSG00000249631	ENST00000823073.1	n.156+2614T>C		intron_variant	Intron 2 of 2
ENSG00000249631	ENST00000823074.1	n.65+3641T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.731 AC: 111095 AN: 151996 Hom.: 41831 Cov.: 33

Gnomad AFR AF: 0.902

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.745

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.718

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

GnomAD4 genome AF: 0.731 AC: 111208 AN: 152114 Hom.: 41881 Cov.: 33 AF XY: 0.723 AC XY: 53782 AN XY: 74338

African (AFR) AF: 0.902 AC: 37463 AN: 41514

American (AMR) AF: 0.547 AC: 8348 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.745 AC: 2586 AN: 3470

East Asian (EAS) AF: 0.536 AC: 2770 AN: 5170

South Asian (SAS) AF: 0.634 AC: 3054 AN: 4814

European-Finnish (FIN) AF: 0.663 AC: 7018 AN: 10578

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.704 AC: 47830 AN: 67982

Other (OTH) AF: 0.716 AC: 1512 AN: 2112

Alfa AF: 0.703 Hom.: 53147

Bravo AF: 0.725

Asia WGS AF: 0.608 AC: 2116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.17
DANN	Benign	0.49
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs6448799; hg19: chr4-11630049;