ENST00000637377.2:n.161+31382T>C

Variant names:

• chr1-58607758-T-C
• rs11207272
• ENST00000637377.2:n.161+31382T>C

Variant summary

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

The ENST00000637377.2(ENSG00000283445):​n.161+31382T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,154 control chromosomes in the GnomAD database, including 4,625 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 0.20 (4625 hom., cov: 32)
• Consequence: ENSG00000283445 ENST00000637377.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299
• Publications: 6 publications found

Genes affected

ENSG00000283445 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000637377.2. 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
	ENSG00000283445	ENST00000637377.2	TSL:5	n.161+31382T>C		intron	N/A
	ENSG00000283445	ENST00000767021.1		n.188+31382T>C		intron	N/A
	ENSG00000283445	ENST00000767022.1		n.142+31382T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31131 AN: 152036 Hom.: 4614 Cov.: 32

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.0548

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.205 AC: 31166 AN: 152154 Hom.: 4625 Cov.: 32 AF XY: 0.199 AC XY: 14772 AN XY: 74396

African (AFR) AF: 0.426 AC: 17661 AN: 41442

American (AMR) AF: 0.125 AC: 1905 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 490 AN: 3472

East Asian (EAS) AF: 0.202 AC: 1046 AN: 5172

South Asian (SAS) AF: 0.162 AC: 782 AN: 4830

European-Finnish (FIN) AF: 0.0548 AC: 582 AN: 10618

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8120 AN: 68008

Other (OTH) AF: 0.184 AC: 389 AN: 2112

Alfa AF: 0.143 Hom.: 3344

Bravo AF: 0.220

Asia WGS AF: 0.200 AC: 695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.2
DANN	Benign	0.79
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs11207272; hg19: chr1-59073430; COSMIC: COSV59945699;