chr5-44982215-A-G

Variant names:

• chr5-44982215-A-G
• rs2067980
• ENST00000780689.1:n.321+11717T>C

Variant summary

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

The ENST00000780689.1(ENSG00000301660):​n.321+11717T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,102 control chromosomes in the GnomAD database, including 2,384 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 0.16 (2384 hom., cov: 32)
• Consequence: ENSG00000301660 ENST00000780689.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.641
• Publications: 8 publications found

Genes affected

ENSG00000301660 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.462 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
ENSG00000301660	ENST00000780689.1	n.321+11717T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24215 AN: 151984 Hom.: 2369 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.159 AC: 24254 AN: 152102 Hom.: 2384 Cov.: 32 AF XY: 0.165 AC XY: 12274 AN XY: 74354

African (AFR) AF: 0.104 AC: 4334 AN: 41514

American (AMR) AF: 0.177 AC: 2700 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 442 AN: 3472

East Asian (EAS) AF: 0.477 AC: 2458 AN: 5148

South Asian (SAS) AF: 0.273 AC: 1313 AN: 4818

European-Finnish (FIN) AF: 0.173 AC: 1829 AN: 10570

Middle Eastern (MID) AF: 0.140 AC: 41 AN: 292

European-Non Finnish (NFE) AF: 0.155 AC: 10562 AN: 67982

Other (OTH) AF: 0.189 AC: 398 AN: 2108

Alfa AF: 0.153 Hom.: 2978

Bravo AF: 0.156

Asia WGS AF: 0.367 AC: 1273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.25
DANN	Benign	0.41
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs2067980; hg19: chr5-44982317;