rs731824

Positions:

• chr1-230887325-C-A
• chr1-230887325-C-T

Variant summary

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

The ENST00000654598.1(ENSG00000288037):​n.241+2172G>T 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 0.577 in 151,916 control chromosomes in the GnomAD database, including 25,613 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 0.58 (25613 hom., cov: 32)
• Consequence: ENST00000654598.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124904547	XR_007066938.1	n.885+2172G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000654598.1	n.241+2172G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87571 AN: 151800 Hom.: 25601 Cov.: 32

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.655

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.577 AC: 87598 AN: 151916 Hom.: 25613 Cov.: 32 AF XY: 0.572 AC XY: 42482 AN XY: 74254

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.730

Gnomad4 EAS AF: 0.460

Gnomad4 SAS AF: 0.676

Gnomad4 FIN AF: 0.522

Gnomad4 NFE AF: 0.629

Gnomad4 OTH AF: 0.624

Alfa AF: 0.547 Hom.: 6377

Bravo AF: 0.571

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.96
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs731824; hg19: chr1-231023071;