1-232886124-C-G

Position:

• chr1-232886124-C-G

Variant summary

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

The ENST00000667494.1(ENSG00000286774):​n.360-9548C>G 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 0.148 in 151,938 control chromosomes in the GnomAD database, including 3,219 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 0.15 (3219 hom., cov: 32)
• Consequence: ENST00000667494.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927711	XR_949278.3	n.963-9548C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000667494.1	n.360-9548C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22511 AN: 151818 Hom.: 3210 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.0202

Gnomad EAS AF: 0.0911

Gnomad SAS AF: 0.0477

Gnomad FIN AF: 0.0601

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0454

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.148 AC: 22561 AN: 151938 Hom.: 3219 Cov.: 32 AF XY: 0.146 AC XY: 10820 AN XY: 74266

Gnomad4 AFR AF: 0.372

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.0202

Gnomad4 EAS AF: 0.0915

Gnomad4 SAS AF: 0.0478

Gnomad4 FIN AF: 0.0601

Gnomad4 NFE AF: 0.0454

Gnomad4 OTH AF: 0.124

Alfa AF: 0.110 Hom.: 246

Bravo AF: 0.170

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9424490; hg19: chr1-233021870;