rs13120644

Variant names:

• chr4-55732335-C-G
• rs13120644
• ENST00000767667.1:n.474-5948G>C

Variant summary

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

The ENST00000767667.1(ENSG00000299956):​n.474-5948G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 151,910 control chromosomes in the GnomAD database, including 14,465 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 (14465 hom., cov: 32)
• Consequence: ENSG00000299956 ENST00000767667.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 0 publications found

Genes affected

ENSG00000299956 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.878 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
ENSG00000299956	ENST00000767667.1	n.474-5948G>C		intron_variant	Intron 4 of 4
ENSG00000299956	ENST00000767668.1	n.485-5948G>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.415 AC: 62994 AN: 151792 Hom.: 14445 Cov.: 32

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.898

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.415 AC: 63051 AN: 151910 Hom.: 14465 Cov.: 32 AF XY: 0.422 AC XY: 31299 AN XY: 74248

African (AFR) AF: 0.282 AC: 11674 AN: 41432

American (AMR) AF: 0.507 AC: 7730 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1844 AN: 3464

East Asian (EAS) AF: 0.899 AC: 4656 AN: 5178

South Asian (SAS) AF: 0.659 AC: 3175 AN: 4818

European-Finnish (FIN) AF: 0.388 AC: 4087 AN: 10536

Middle Eastern (MID) AF: 0.500 AC: 146 AN: 292

European-Non Finnish (NFE) AF: 0.421 AC: 28570 AN: 67916

Other (OTH) AF: 0.443 AC: 933 AN: 2106

Alfa AF: 0.420 Hom.: 1746

Bravo AF: 0.415

Asia WGS AF: 0.763 AC: 2653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.30
DANN	Benign	0.54
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs13120644; hg19: chr4-56598502;