chr1-60814879-T-C

Position:

• chr1-60814879-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000423403.1(ENSG00000231252):​n.249+10457A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.063 in 152,292 control chromosomes in the GnomAD database, including 398 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 0.063 (398 hom., cov: 32)
• Consequence: ENSG00000231252 ENST00000423403.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.45

Genes affected

ENSG00000231252 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.1 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101926964	NR_110628.1	n.249+10457A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000231252	ENST00000423403.1	n.249+10457A>G		intron_variant		2
ENSG00000231252	ENST00000634701.1	n.274+10457A>G		intron_variant		5
ENSG00000231252	ENST00000635290.1	n.296+10457A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0630 AC: 9590 AN: 152174 Hom.: 398 Cov.: 32

Gnomad AFR AF: 0.0186

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0711

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.0313

Gnomad FIN AF: 0.0516

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0896

Gnomad OTH AF: 0.0661

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

GnomAD4 genome AF: 0.0630 AC: 9592 AN: 152292 Hom.: 398 Cov.: 32 AF XY: 0.0615 AC XY: 4581 AN XY: 74466

Gnomad4 AFR AF: 0.0185

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.0711

Gnomad4 EAS AF: 0.00251

Gnomad4 SAS AF: 0.0313

Gnomad4 FIN AF: 0.0516

Gnomad4 NFE AF: 0.0896

Gnomad4 OTH AF: 0.0645

Alfa AF: 0.0820 Hom.: 296

Bravo AF: 0.0666

Asia WGS AF: 0.0220 AC: 78 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	13
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs665036; hg19: chr1-61280551;