rs72717009

Variant names:

• chr1-161435263-C-T
• rs72717009
• ENST00000636824.1:n.118-1368G>A

Variant summary

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

The ENST00000636824.1(ENSG00000283317):​n.118-1368G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 152,170 control chromosomes in the GnomAD database, including 1,649 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 0.14 (1649 hom., cov: 32)
• Consequence: ENSG00000283317 ENST00000636824.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 20 publications found

Genes affected

ENSG00000283317 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.193 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
ENSG00000283317	ENST00000636824.1	n.118-1368G>A		intron_variant	Intron 1 of 1	4
ENSG00000283360	ENST00000637155.1	n.55-7244G>A		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20927 AN: 152052 Hom.: 1633 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.0250

Gnomad SAS AF: 0.0608

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.138 AC: 20985 AN: 152170 Hom.: 1649 Cov.: 32 AF XY: 0.141 AC XY: 10464 AN XY: 74370

African (AFR) AF: 0.168 AC: 6995 AN: 41516

American (AMR) AF: 0.199 AC: 3037 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 880 AN: 3470

East Asian (EAS) AF: 0.0249 AC: 129 AN: 5188

South Asian (SAS) AF: 0.0617 AC: 298 AN: 4828

European-Finnish (FIN) AF: 0.143 AC: 1512 AN: 10586

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.114 AC: 7754 AN: 67990

Other (OTH) AF: 0.135 AC: 285 AN: 2112

Alfa AF: 0.121 Hom.: 347

Bravo AF: 0.144

Asia WGS AF: 0.0570 AC: 200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.46
DANN	Benign	0.25
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs72717009; hg19: chr1-161405053;