17-6438550-A-G

Variant names:

• chr17-6438550-A-G
• rs58926603
• XR_001752776.2:n.419-1213T>C

Variant summary

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

The XR_001752776.2(LOC107985017):​n.419-1213T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.48 (11954 hom., cov: 14)
• Consequence: LOC107985017 XR_001752776.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.995
• Publications: 2 publications found

Genes affected

LOC107985017 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985017	XR_001752776.2	n.419-1213T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.475 AC: 50773 AN: 106852 Hom.: 11953 Cov.: 14

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.558

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.475 AC: 50776 AN: 106880 Hom.: 11954 Cov.: 14 AF XY: 0.482 AC XY: 23629 AN XY: 49044

African (AFR) AF: 0.577 AC: 15212 AN: 26384

American (AMR) AF: 0.443 AC: 3897 AN: 8794

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1469 AN: 3068

East Asian (EAS) AF: 0.613 AC: 2180 AN: 3558

South Asian (SAS) AF: 0.529 AC: 1580 AN: 2984

European-Finnish (FIN) AF: 0.535 AC: 1864 AN: 3486

Middle Eastern (MID) AF: 0.567 AC: 85 AN: 150

European-Non Finnish (NFE) AF: 0.419 AC: 23599 AN: 56270

Other (OTH) AF: 0.464 AC: 658 AN: 1418

Alfa AF: 0.463 Hom.: 1286

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.57
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs58926603; hg19: chr17-6341870; COSMIC: COSV51505823;