rs4072643

Positions:

• chr1-178565086-C-T

Variant summary

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

The XR_922315.3(LOC105371632):​n.12569-5078G>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 0.0746 in 152,242 control chromosomes in the GnomAD database, including 1,288 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 0.075 (1288 hom., cov: 32)
• Consequence: LOC105371632 XR_922315.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.392

Genes affected

LOC105371632 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105371632	XR_922315.3	n.12569-5078G>A		intron_variant, non_coding_transcript_variant
LOC105371632	XR_007066747.1	n.2972G>A		non_coding_transcript_exon_variant	4/4
LOC105371632	XR_922313.3	n.12570-5078G>A		intron_variant, non_coding_transcript_variant
LOC105371632	XR_922314.3	n.686-5078G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0744 AC: 11322 AN: 152124 Hom.: 1280 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0401

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0188

Gnomad FIN AF: 0.00452

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.00729

Gnomad OTH AF: 0.0675

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

GnomAD4 genome AF: 0.0746 AC: 11361 AN: 152242 Hom.: 1288 Cov.: 32 AF XY: 0.0723 AC XY: 5380 AN XY: 74438

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.0400

Gnomad4 ASJ AF: 0.0173

Gnomad4 EAS AF: 0.000385

Gnomad4 SAS AF: 0.0184

Gnomad4 FIN AF: 0.00452

Gnomad4 NFE AF: 0.00729

Gnomad4 OTH AF: 0.0668

Alfa AF: 0.0219 Hom.: 231

Bravo AF: 0.0867

Asia WGS AF: 0.0230 AC: 80 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.9
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4072643; hg19: chr1-178534221;