1-56100245-G-T

Position:

• chr1-56100245-G-T

Variant summary

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

The XR_001738064.2(LOC105378741):​n.166-1412C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,096 control chromosomes in the GnomAD database, including 5,712 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 0.25 (5712 hom., cov: 32)
• Consequence: LOC105378741 XR_001738064.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26

Genes affected

LOC105378741 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378741	XR_001738064.2	n.166-1412C>A		intron_variant, non_coding_transcript_variant
LOC105378741	XR_001738063.2	n.228-1412C>A		intron_variant, non_coding_transcript_variant
LOC105378741	XR_001738065.2	n.228-1412C>A		intron_variant, non_coding_transcript_variant
LOC105378741	XR_001738066.2	n.228-1412C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37936 AN: 151978 Hom.: 5717 Cov.: 32

Gnomad AFR AF: 0.0695

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.249 AC: 37928 AN: 152096 Hom.: 5712 Cov.: 32 AF XY: 0.248 AC XY: 18414 AN XY: 74358

Gnomad4 AFR AF: 0.0694

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.327

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.295

Alfa AF: 0.231 Hom.: 977

Bravo AF: 0.245

Asia WGS AF: 0.221 AC: 772 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	16
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1412216; hg19: chr1-56565917;