chr1-161493811-G-A

Position:

• chr1-161493811-G-A

Variant summary

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

The XR_922214.3(LOC105371473):​n.1903+192G>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 0.569 in 152,070 control chromosomes in the GnomAD database, including 25,061 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 (25061 hom., cov: 33)
• Consequence: LOC105371473 XR_922214.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295

Genes affected

LOC105371473 (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 (NFE) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105371473	XR_922214.3	n.1903+192G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86412 AN: 151952 Hom.: 25056 Cov.: 33

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.604

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.569 AC: 86469 AN: 152070 Hom.: 25061 Cov.: 33 AF XY: 0.565 AC XY: 41983 AN XY: 74334

Gnomad4 AFR AF: 0.543

Gnomad4 AMR AF: 0.604

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.248

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.584

Gnomad4 NFE AF: 0.611

Gnomad4 OTH AF: 0.564

Alfa AF: 0.582 Hom.: 4203

Bravo AF: 0.571

Asia WGS AF: 0.372 AC: 1297 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	1.0
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7512140; hg19: chr1-161463601;