chr1-72745942-A-C

Position:

• chr1-72745942-A-C

Variant summary

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

The NR_188684.1(LOC105378798):​n.202+3224T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0841 in 152,100 control chromosomes in the GnomAD database, including 1,584 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 0.084 (1584 hom., cov: 32)
• Consequence: LOC105378798 NR_188684.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27

Genes affected

ENSG00000225087 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378798	NR_188684.1	n.202+3224T>G		intron_variant
LOC105378798	NR_188685.1	n.230+3224T>G		intron_variant
LOC105378798	NR_188686.1	n.202+3224T>G		intron_variant
LOC105378798	NR_188687.1	n.202+3224T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000225087	ENST00000654386.1	n.436+3224T>G		intron_variant
ENSG00000286863	ENST00000659328.1	n.398-7726A>C		intron_variant
ENSG00000225087	ENST00000660076.1	n.207+3224T>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0840 AC: 12759 AN: 151982 Hom.: 1583 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0328

Gnomad ASJ AF: 0.0219

Gnomad EAS AF: 0.00406

Gnomad SAS AF: 0.00703

Gnomad FIN AF: 0.00574

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00874

Gnomad OTH AF: 0.0627

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

GnomAD4 genome AF: 0.0841 AC: 12790 AN: 152100 Hom.: 1584 Cov.: 32 AF XY: 0.0809 AC XY: 6017 AN XY: 74368

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.0328

Gnomad4 ASJ AF: 0.0219

Gnomad4 EAS AF: 0.00407

Gnomad4 SAS AF: 0.00704

Gnomad4 FIN AF: 0.00574

Gnomad4 NFE AF: 0.00874

Gnomad4 OTH AF: 0.0620

Alfa AF: 0.0567 Hom.: 127

Bravo AF: 0.0954

Asia WGS AF: 0.0280 AC: 98 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.43
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10493510; hg19: chr1-73211625;