rs965972

chr1-193494720-G-A

Variant summary

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

The ENST00000656143.1(ENSG00000227240):n.153+21344G>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 0.865 in 151,810 control chromosomes in the GnomAD database, including 58,152 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 0.86 (58152 hom., cov: 29)
• Consequence: ENST00000656143.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.96 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904475	XR_007066777.1	n.5234+21344G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000656143.1	n.153+21344G>A		intron_variant, non_coding_transcript_variant
	ENST00000691564.1	n.252+11929G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.865 AC: 131164 AN: 151692 Hom.: 58115 Cov.: 29

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.992

Gnomad AMR AF: 0.866

Gnomad ASJ AF: 0.935

Gnomad EAS AF: 0.681

Gnomad SAS AF: 0.909

Gnomad FIN AF: 0.990

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.966

Gnomad OTH AF: 0.892

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

GnomAD4 genome AF: 0.865 AC: 131246 AN: 151810 Hom.: 58152 Cov.: 29 AF XY: 0.865 AC XY: 64171 AN XY: 74202

Gnomad4 AFR AF: 0.671

Gnomad4 AMR AF: 0.866

Gnomad4 ASJ AF: 0.935

Gnomad4 EAS AF: 0.680

Gnomad4 SAS AF: 0.909

Gnomad4 FIN AF: 0.990

Gnomad4 NFE AF: 0.966

Gnomad4 OTH AF: 0.895

Alfa AF: 0.931 Hom.: 35198

Bravo AF: 0.842

Asia WGS AF: 0.846 AC: 2943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.3
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs965972; hg19: chr1-193463850;