1-189559313-T-C

Variant names:

• chr1-189559313-T-C
• rs382645
• XR_002958413.2:n.483-9016T>C

Variant summary

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

The XR_002958413.2(LOC105371657):​n.483-9016T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 151,810 control chromosomes in the GnomAD database, including 19,923 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 0.51 (19923 hom., cov: 32)
• Consequence: LOC105371657 XR_002958413.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.201

Genes affected

LOC105371657 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371657	XR_002958413.2	n.483-9016T>C		intron_variant	Intron 3 of 4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77559 AN: 151694 Hom.: 19915 Cov.: 32

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.511 AC: 77595 AN: 151810 Hom.: 19923 Cov.: 32 AF XY: 0.513 AC XY: 38063 AN XY: 74192

Gnomad4 AFR AF: 0.521

Gnomad4 AMR AF: 0.458

Gnomad4 ASJ AF: 0.463

Gnomad4 EAS AF: 0.596

Gnomad4 SAS AF: 0.435

Gnomad4 FIN AF: 0.593

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.504

Alfa AF: 0.499 Hom.: 8939

Bravo AF: 0.507

Asia WGS AF: 0.452 AC: 1571 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.5
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs382645; hg19: chr1-189528443; COSMIC: COSV60001869;