chr1-39827026-A-C

Position:

• chr1-39827026-A-C

Variant summary

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

The XR_947221.3(LOC105378667):​n.428+1323A>C 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 0.392 in 152,142 control chromosomes in the GnomAD database, including 12,009 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 0.39 (12009 hom., cov: 33)
• Consequence: LOC105378667 XR_947221.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125

Genes affected

LOC105378667 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378667	XR_947221.3	n.428+1323A>C		intron_variant, non_coding_transcript_variant
LOC105378667	XR_947222.3	n.172+1323A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59538 AN: 152024 Hom.: 11977 Cov.: 33

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.392 AC: 59625 AN: 152142 Hom.: 12009 Cov.: 33 AF XY: 0.391 AC XY: 29106 AN XY: 74376

Gnomad4 AFR AF: 0.474

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.393

Gnomad4 EAS AF: 0.549

Gnomad4 SAS AF: 0.442

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.363

Alfa AF: 0.382 Hom.: 1626

Bravo AF: 0.403

Asia WGS AF: 0.531 AC: 1845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.1
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs230273; hg19: chr1-40292698;