rs965972

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904475	XR_007066777.1	n.5234+21344G>A		intron_variant	Intron 3 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000227240	ENST00000656143.2	n.153+21344G>A		intron_variant	Intron 1 of 5
ENSG00000286285	ENST00000691564.2	n.282+11929G>A		intron_variant	Intron 1 of 1
ENSG00000286285	ENST00000767304.1	n.345+36970G>A		intron_variant	Intron 3 of 3

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 v4.3

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;