chr1-221378197-C-A

Position:

• chr1-221378197-C-A

Variant summary

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

The XR_922621.2(LOC105372932):​n.455-1565C>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 0.302 in 151,946 control chromosomes in the GnomAD database, including 7,963 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 0.30 (7963 hom., cov: 32)
• Consequence: LOC105372932 XR_922621.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72

Genes affected

LOC105372932 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372932	XR_922621.2	n.455-1565C>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45859 AN: 151828 Hom.: 7968 Cov.: 32

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.652

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.302 AC: 45871 AN: 151946 Hom.: 7963 Cov.: 32 AF XY: 0.307 AC XY: 22826 AN XY: 74258

Gnomad4 AFR AF: 0.401

Gnomad4 AMR AF: 0.352

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.653

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.277

Alfa AF: 0.244 Hom.: 6337

Bravo AF: 0.317

Asia WGS AF: 0.493 AC: 1714 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.036
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12733856; hg19: chr1-221551539;