6-19051464-C-T

Variant names:

• chr6-19051464-C-T
• rs926274
• XR_001744010.1:n.398+25677C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001744010.1(LOC105374958):​n.398+25677C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 151,878 control chromosomes in the GnomAD database, including 24,798 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 0.57 (24798 hom., cov: 31)
• Consequence: LOC105374958 XR_001744010.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145

Genes affected

LOC105374958 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374958	XR_001744010.1	n.398+25677C>T		intron_variant	Intron 3 of 4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86401 AN: 151760 Hom.: 24797 Cov.: 31

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.569 AC: 86433 AN: 151878 Hom.: 24798 Cov.: 31 AF XY: 0.571 AC XY: 42417 AN XY: 74252

Gnomad4 AFR AF: 0.525

Gnomad4 AMR AF: 0.511

Gnomad4 ASJ AF: 0.541

Gnomad4 EAS AF: 0.564

Gnomad4 SAS AF: 0.615

Gnomad4 FIN AF: 0.671

Gnomad4 NFE AF: 0.592

Gnomad4 OTH AF: 0.589

Alfa AF: 0.581 Hom.: 50530

Bravo AF: 0.552

Asia WGS AF: 0.579 AC: 2014 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.2
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs926274; hg19: chr6-19051695;