chr5-140351647-T-C

Variant names:

• chr5-140351647-T-C
• rs6879217
• ENST00000520443.2:n.514-3107A>G

Variant summary

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

The ENST00000520443.2(ENSG00000253965):​n.514-3107A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 152,092 control chromosomes in the GnomAD database, including 13,610 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 0.41 (13610 hom., cov: 32)
• Consequence: ENSG00000253965 ENST00000520443.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.783
• Publications: 9 publications found

Genes affected

ENSG00000253965 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.535 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
ENSG00000253965	ENST00000520443.2	n.514-3107A>G		intron_variant	Intron 1 of 1	4
ENSG00000253965	ENST00000783095.1	n.282+1144A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62789 AN: 151974 Hom.: 13617 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.413 AC: 62788 AN: 152092 Hom.: 13610 Cov.: 32 AF XY: 0.411 AC XY: 30579 AN XY: 74348

African (AFR) AF: 0.297 AC: 12325 AN: 41492

American (AMR) AF: 0.453 AC: 6922 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1553 AN: 3470

East Asian (EAS) AF: 0.552 AC: 2859 AN: 5184

South Asian (SAS) AF: 0.481 AC: 2315 AN: 4810

European-Finnish (FIN) AF: 0.364 AC: 3852 AN: 10568

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.459 AC: 31212 AN: 67968

Other (OTH) AF: 0.443 AC: 935 AN: 2110

Alfa AF: 0.444 Hom.: 26214

Bravo AF: 0.419

Asia WGS AF: 0.464 AC: 1617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	14
DANN	Benign	0.79
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs6879217; hg19: chr5-139731232;