rs6449612

Variant names:

• chr5-51405268-C-T
• rs6449612
• ENST00000730931.1:n.388-10841G>A

Variant summary

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

The ENST00000730931.1(ENSG00000288035):​n.388-10841G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 151,918 control chromosomes in the GnomAD database, including 14,101 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 0.42 (14101 hom., cov: 32)
• Consequence: ENSG00000288035 ENST00000730931.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.760
• Publications: 4 publications found

Genes affected

ENSG00000288035 (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 = 0.551 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288035	ENST00000730931.1	n.388-10841G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63538 AN: 151800 Hom.: 14083 Cov.: 32

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.419 AC: 63596 AN: 151918 Hom.: 14101 Cov.: 32 AF XY: 0.411 AC XY: 30540 AN XY: 74250

African (AFR) AF: 0.557 AC: 23085 AN: 41438

American (AMR) AF: 0.370 AC: 5646 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 997 AN: 3472

East Asian (EAS) AF: 0.176 AC: 909 AN: 5172

South Asian (SAS) AF: 0.309 AC: 1486 AN: 4816

European-Finnish (FIN) AF: 0.379 AC: 3997 AN: 10556

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.386 AC: 26189 AN: 67896

Other (OTH) AF: 0.394 AC: 830 AN: 2106

Alfa AF: 0.394 Hom.: 6342

Bravo AF: 0.423

Asia WGS AF: 0.293 AC: 1020 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	0.31
DANN	Benign	0.43
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs6449612; hg19: chr5-50701102;