chr1-172711891-T-C

Variant names:

• chr1-172711891-T-C
• rs12068671
• ENST00000725727.1:n.69+41292T>C

Variant summary

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

The ENST00000725727.1(ENSG00000224000):​n.69+41292T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 151,972 control chromosomes in the GnomAD database, including 4,733 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 0.23 (4733 hom., cov: 31)
• Consequence: ENSG00000224000 ENST00000725727.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.110
• Publications: 16 publications found

Genes affected

ENSG00000224000 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000224000	ENST00000725727.1	n.69+41292T>C		intron_variant	Intron 1 of 1
ENSG00000224000	ENST00000725728.1	n.108+32189T>C		intron_variant	Intron 1 of 1
ENSG00000224000	ENST00000725729.1	n.37-28322T>C		intron_variant	Intron 1 of 2
ENSG00000224000	ENST00000725730.1	n.40-28322T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34222 AN: 151854 Hom.: 4729 Cov.: 31

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.225 AC: 34254 AN: 151972 Hom.: 4733 Cov.: 31 AF XY: 0.221 AC XY: 16396 AN XY: 74304

African (AFR) AF: 0.386 AC: 15967 AN: 41416

American (AMR) AF: 0.156 AC: 2383 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 740 AN: 3468

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5176

South Asian (SAS) AF: 0.114 AC: 548 AN: 4800

European-Finnish (FIN) AF: 0.169 AC: 1787 AN: 10556

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12209 AN: 67956

Other (OTH) AF: 0.196 AC: 411 AN: 2096

Alfa AF: 0.220 Hom.: 596

Bravo AF: 0.232

Asia WGS AF: 0.0710 AC: 249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	10
DANN	Benign	0.63
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs12068671; hg19: chr1-172681031;