chr1-193494720-G-A

Variant names:

• chr1-193494720-G-A
• rs965972
• ENST00000656143.2:n.153+21344G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000656143.2(ENSG00000227240):​n.153+21344G>A variant causes a intron 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: ENSG00000227240 ENST00000656143.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190
• Publications: 10 publications found

Genes affected

ENSG00000227240 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656143.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000227240	ENST00000656143.2		n.153+21344G>A		intron	N/A
	ENSG00000286285	ENST00000691564.2		n.282+11929G>A		intron	N/A
	ENSG00000286285	ENST00000767304.1		n.345+36970G>A		intron	N/A

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

African (AFR) AF: 0.671 AC: 27732 AN: 41300

American (AMR) AF: 0.866 AC: 13175 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.935 AC: 3248 AN: 3472

East Asian (EAS) AF: 0.680 AC: 3505 AN: 5154

South Asian (SAS) AF: 0.909 AC: 4354 AN: 4792

European-Finnish (FIN) AF: 0.990 AC: 10457 AN: 10566

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.966 AC: 65730 AN: 68018

Other (OTH) AF: 0.895 AC: 1876 AN: 2096

Alfa AF: 0.930 Hom.: 38852

Bravo AF: 0.842

Asia WGS AF: 0.846 AC: 2943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.58
PhyloP100		0.019

Splicing

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

Other links and lift over

dbSNP: rs965972; hg19: chr1-193463850;